We'll be live-blogging the aftermath of this incident throughout the day; keep checking back for international reaction, news from our correspondents on the ground, photos and video. (All times are GMT, except where noted.)
8:45pm: William Hague, the British foreign secretary, says one Briton was among the injured on board and calls for an independent inquiry.
"So far we have been given access to one UK national who was injured, we don't know yet for certain about any deaths," Hague told journalists.
"We know there may have been UK nationals who have been detained and we are seeking consular access."
8:05pm: Ehud Barak, the Israeli defence minister, has called US Secretary of State Hillary Clinton and National Security Advisory James Jones on Monday to brief them on the assault.
A statement from Barak's office said he had told them that the raid was in keeping with maritime law.
"The passengers on the Marmara beat our soldiers with every object they had and wounded some of them," the statement quoted him as saying.
"The soldiers defended themselves."
7.53pm: Oscar Fernandez-Taranco, the chief foreign policy official of the United Nations, asks Israel to end its "counterproductive" and "unacceptable" blockade on Gaza in the emergency UN Security Council meeting.
7:30pm: Following a 90-minute open meeting, the UN Security Council goes into closed-door consultations.
Ahmet Davutoglu, Turkey's foreign minister, urged the council to adopt a presidential statement circulated by Turkey which would condemn the raid by Israeli forces "in the strongest terms" as a violation of international law.
It would also express deep regret at the loss of life and call for Ban Ki-moon, the UN secretary-general, to undertake "an independent international investigation" and consider the issue of compensation.
The draft also calls on Israel to lift its blockade of Gaza and immediately release the ships and civilians it is holding.
7:05pm: Mohammad Dahlan, a senior member of Fatah, just announced that the party will send a delegation to Gaza to meet with Hamas for reconciliation talks, and that the Palestinian Authority will push for a UN Security Council resolution on lifting the blockade of Gaza.
Hamas and Fatah have been bitterly at odds since Hamas took control of Gaza in 2007, and months of recent reconciliation talks haven't led anywhere. So a Fatah delegation to Gaza could be a significant step.
6:53pm: Ambassadors from the 27 EU countries have issued a statement:
The EU condemns the use of violence that has produced a high number of victims among the members of the flottilla and demands an immediate, full and impartial inquiry into the events and the circumstances surrounding it," the ambassadors said in a statement.
Adding that the humanitarian situation in Gaza remains a great concern, the ambassdors said the "EU does not accept the continued policy of closure, it is unacceptable and politically counterproductive, we need to urgently achieve a durable solution to the situation in Gaza."
6:24pm: Three Israeli human rights groups seek a court order for the state to give the names of the people killed or wounded when commandos stormed the ships.
The petition was submitted by Adalah, the Public Committee Against Torture in Israel and Physicians for Human Rights-Israel.
6:12pm: Recep Tayyip Erdogan, Turkey's prime minister, says the flotilla was carefully inspected before departure:
I want to say to the world, to the heads of state and the governments, that these boats that left from Turkey and other countries were checked in a strict way under the framework of the rules of international navigation and were only loaded with humanitarian aid."
There was no one on board "other than civilian volunteers" he said.
5:53pm: The United Nations Security Council has begun an emergency session to discuss the Israeli raid.
5:35pm: Al Jazeera's Sherine Tadros says there are reports of a rocket landing in the southern Israeli city of Ashkelon.
4:59pm: That's all for me this evening; a few colleagues will be taking over the live-blog for the rest of the night, and we'll be covering this story lots more tomorrow, I'm sure.
I've added a few links above that will jump you down to some of the more notable updates from the live blog.
4:37pm: The Turkish newspaper Hurriyet has a round-up of reactions from the familiesof activists on board the ships, many of whom are worried about their missing relatives. There's still been no communication with any of the passengers, activists and journalists alike.
4:32pm: This has been posted for a few hours, but I put together a quick piece for our focus section looking at the consequences of Israel's Gaza blockade -- which, despite the oft-repeated Israeli claim that there's "no humanitarian crisis in Gaza," has caused malnutrition, poor medical care, frequent blackouts and countless avoidable deaths.
4:21pm: From the White House press office, a "readout" (summary) of Obama's call with Netanyahu:
This morning between 10:00 and 10:15 AM CDT, the President spoke by phone with Prime Minister Netanyahu. He said he understood the Prime Minister's decision to return immediately to Israel to deal with today's events. They agreed to reschedule their meeting at the first opportunity. The President expressed deep regret at the loss of life in today's incident, and concern for the wounded, many of whom are being treated in Israeli hospitals. The President also expressed the importance of learning all the facts and circumstances around this morning's tragic events as soon as possible.
4:19pm: Raed Salah is "in good health," according to Al Jazeera's Ayman Mohyeldin, who talked with Salah's spokesman, Mahmoud Abu Attar.
Salah is still on board the Mavi Marmara, which is expected to arrive at Ashdod port momentarily.
4:18pm: The IDF just released another video, which shows two wounded Israeli soldiers (their conditions are unclear) and several of the weapons allegedly found on board the ship.
The collection of weapons includes a crudely-made slingshot, a thin metal pipe, and what appears to be a plastic bag filled with marbles. Nowhere is there evidence of guns, or even of knives. Most of the weapons appear to be improvised out of materials found on board the ship.
4:04pm: The protests which began in the Middle East and Asia this morning have spread to Europe.
Protesters outside Downing Street in London [AFP]
Large protests have been reported in London, where demonstrators gathered near the prime minister's residence on Downing Street, and in Paris.
Jerzy Buzek, the president of the European Parliament, condemned the "disproportionate action" taken by the Israeli army and urged Catherine Ashton, the EU's foreign policy chief, to push Israel to lift the blockade on Gaza.
3:59pm: Netanyahu canceled his 3pm press conference, but he did make brief remarks at a photo op with Canadian prime minister Stephen Harper.
Netanyahu said he regretted the loss of life during the Israeli raid on the flotilla, and that he spoke with US president Barack Obama. He didn't elaborate on the content of their conversation, though, except to say they agreed to reschedule their planned meeting "for the earliest date possible."
Netanyahu also defended the actions of the Israeli soldiers on board the ships, saying they were "defending themselves" after being attacked.
3:52pm: The Israeli navy is holding a press conference right now in the port city of Ashdod, where most of the seized boats have been towed.
14 of the detained activists have agreed to be deported, according to the Israeli navy, and they will be put on planes and flown back to their home countries; another 50 are resisting deportation, and they're being transported to a prison in Beersheba, in southern Israel.
3:46pm: Amr Moussa, the secretary-general of the Arab League, was interviewed on Al Jazeera a few moments ago. He talked briefly about tomorrow's scheduled Arab League meeting.
It will focus on two things: The crime itself, this military attack against people... and the message that there is no use in making peace with Israel, because Israeli policy is not interested in peace.
3:41pm: We're getting reports of fighting between Israeli police and Palestinian citizens of Israel in the northern city of Umm al-Fahm, the hometown of Raed Salah, the Islamic Movement of Israel activist (who may or may not have been seriously injured in the flotilla attack, according to conflicting reports).
There's also word of a large rally scheduled to start in Haifa in about 20 minutes, at 4pm GMT.
3:30pm: The Palestinian Ma'an News Agency pieced together a nine-minute video, using clips from Al Jazeera and other journalists on board, showing the minutes before Israeli commandos took control of the Mavi Marmara.
It's hard to say whether the video is sequential, and whether it happened before or after the official IDF video we embedded below (see 1:59pm update). One person has already been killed in this video, but the relatively low casualty count (compared to the final death toll) suggests there hasn't yet been a large shootout on the ship.
3:13pm: Recep Tayyip Erdogan, Turkey's prime minister, has described the flotilla attack as "inhuman state terror."
3:00pm: Four of the flotilla's six boats have now docked in Ashdod, according to Al Jazeera's Sherine Tadros. Still no word from any of the passengers on board.
2:56pm: Israeli prime minister Binyamin Netanyahu had been scheduled to hold a press conference in Canada at 3pm GMT (just a few minutes from now). That press conference has been abruptly canceled; Netanyahu's staff says he's leaving early to return to Israel.
Meanwhile, the UN Security Council has officially scheduled a meeting to discuss the flotilla attack. It will start at 1pm local time (5pm GMT).
Palestinians throw stones in Jerusalem [AFP]
2:48pm: Global Voices Online is doing a good job rounding up blog and Twitter reactions to the flotilla attack. You notice quickly -- from GV's summary, or from following the #flotilla hashtag on Twitter -- that this story has become a galvanizing issue for many people.
I'll just say that the bottom line for Washington is that the U.S. can not ignore this or try to hope that it will pass quickly so that it can resume business as usual. It is rapidly spiraling into one of the most intensely galvanizing issues in the Arab media -- and around the world -- since the Israeli war on Gaza itself. If Obama goes ahead and meets with Netanyahu as if nothing happened, then his administration's outreach to the Muslim communities of the world is effectively over.
The White House has not exactly rushed to comment on the flotilla attack. We reported a brief one-sentence statement this morning (see 11:51am post); that's all we've heard so far.
(Netanyahu, we should note, announced about 30 minutes ago that he will not visit Washington as planned tomorrow.)
2:34pm: In addition to the Israeli army's official statement and video (see 1:59pm update), several Israeli military journalists are also publishing accounts of the raid.
Ha'aretz quotes Israeli commandos who describe the landing as a "lynching"; Ron Ben Yishai, Yedioth Ahronoth's military correspondent, calls it a "brutal ambush at sea."
Navy commandoes slid down to the vessel one by one, yet then the unexpected occurred: The passengers that awaited them on the deck pulled out bats, clubs, and slingshots with glass marbles, assaulting each soldier as he disembarked. The fighters were nabbed one by one and were beaten up badly, yet they attempted to fight back.
The sourcing on these reports is unclear -- was Yishai traveling with the commandos? were the Ha'aretz correspondents? -- so it's hard to tell whether these reports are based on any first-hand observation, or merely official statements from the defence ministry.
2:29pm: Salam Fayyad, the Palestinian prime minister, told Al Jazeera that the "most appropriate response" to Israel's attack on the flotilla would be for Hamas and Fatah to put aside their differences and sign a reconciliation deal.
The government condemns this crime, which reflects Israel’s disregard of international law and customs. It also reveals the urgent need to putting an end to the hostile policies of the Israeli government, starting with the unconditional lifting of the unjust siege on the Gaza Strip.
The statement is quite mocking of the activists on the flotilla, referring to them as "human rights knights" - not a title they ever appropriated for themselves - and dismissing them as "terror-supporters and anarchists."
2:09pm: Netanyahu has canceled his scheduled trip to Washington - he was supposed to meet with Obama tomorrow - and plans to return to Jerusalem.
The video does clearly show activists attacking several of the soldiers landing on the ship. One of them is thrown from the upper deck of the ship to the lower deck; another is attacked with some kind of metal pole.
But a few caveats: The video is grainy and sometimes hard to decipher, because it was shot at a distance. The text overlaid on the video influences your perception (as one Israeli journalist just remarked, "it helpfully explain[s] what you're supposed to see").
And, of course, the clip only contains the footage the IDF wanted to release; we don't know what happened before or after this 60 seconds of video.
1:50pm: As per Lebanon's request (see our 11:18am update), the United Nations Security Council will meet this afternoon to discuss the flotilla attack. No exact time yet for the meeting.
1:50pm: As per Lebanon's request (see our 11:18am update), the United Nations Security Council will meet this afternoon to discuss the flotilla attack. No exact time yet for the meeting.
1:35pm: A group of Israeli activists affiliated with Hadash - the Jewish-Arab socialist party - is planning a rally tonight in front of the defence ministry building in Tel Aviv.
"The violent takeover of the Flotilla expresses the government's lost path, pushing it to acts of madness, killing and political suicide," the group wrote in a Facebook announcement about the rally.
12:50pm: Careful wording from Catherine Ashton, the European Union foreign policy chief, who said she "deeply regrets the loss of life as a result of the Israeli military operation."
The EU strongly condemns any acts of violence and deplores any excessive use of force. In this regard, on behalf of the EU, the High Representative is requesting a full immediate enquiry by the Israeli authorities.
Her language is a bit hedged, similar to the brief White House statement we copied earlier: Ashton doesn't specifically call the flotilla attack an "excessive use of force."
Ashton also calls the continued "policy of closure of Gaza" unacceptable and "politically counterproductive."
"Israeli forces appear clearly to have used excessive force," said Malcolm Smart, Amnesty International’s director for the Middle East and North Africa. "Israel says its forces acted in self-defence, alleging that they were attacked by protestors, but it begs credibility that the level of lethal force used by Israeli troops could have been justified. It appears to have been out of all proportion to any threat posed."
The group called on Israel to reveal the rules of engagement it issued to its commandos.
12:38pm: Israeli prime minister Binyamin Netanyahu spoke this afternoon with defence minister Ehud Barak, army chief of staff Lt Gen Gabi Ashkenazi, and several other Israeli officials, according to a statement from Netanyahu's office.
The prime minister "reiterated his full backing for the IDF."
Netanyahu is currently in Canada, where he's been traveling for the last few days. He's expected to issue a longer statement to the press this afternoon.
12:30pm: The flotilla story continues to command a lot of attention in the regional media, not just in the Arabic press, but also in Turkey.
11:51am: Bill Burton, a spokesman for the White House, issued a very short statement this morning from Chicago, where President Obama is spending the weekend:
The United States deeply regrets the loss of life and injuries sustained, and is currently working to understand the circumstances surrounding this tragedy.
The US is just waking up; I'm sure we'll see a longer White House statement today, plus further reactions from members of Congress, lobbying groups and other organizations. Remember, though, that this is a holiday weekend in the US -- today is Memorial Day -- so this story might receive less attention than it ordinarily would.
11:28am: Nabil al-Sharif, Jordan's minister of communication and media affairs, gave a statement to reporters a few minutes ago; he called the Israeli attack an "ugly, unacceptable crime."
Jordan is very concerned, and is following up on the fate of its 25 passengers aboard the flotilla, and holds Israel completely accountable and responsible for any harm caused to the Jordanians on board.
Jordan calls on the international community to take firm and immediate action to pressure Israel to lift its siege on Gaza.
A few other reactions: A spokesman for German chancellor Angela Merkel said that, at first glance, the raid does not appear "proportional," which would make it a violation of international law; Britain's foreign secretary, William Hague, said there was a "clear need for Israel to act with restraint"; South Africa condemned the attacks; and Austria's foreign ministry has summoned the Israeli ambassador.
11:18am: Lebanon's foreign minister, Ali al-Shami, said a few moments ago that his government will ask the UN Security Council to condemn the Israeli attack.
Protesters in Amman, Jordan [AFP]
Lebanon currently holds the rotating presidency of the council -- but that presidency expires at the end of May.
11:15am: The Egyptian foreign ministry has summoned Israel's ambassador to Egypt, according to Egyptian state television.
11:11am: Ban Ki-moon, the United Nations secretary-general, called for a full investigation of the flotilla attack during a press conference today in Kampala, Uganda.
It is vital that there is a full investigation to determine exactly how this bloodshed took place. I believe Israel must urgently provide a full explanation.
Other UN officials have offered harsher statements: Robert Serry, the UN special coordinator for the Middle East peace process, and Filippo Grandi, the commissioner-general of UNRWA, said they were "shocked" by the attack and "condemn[ed] the violence."
11:06am: Turkey's prime minister, Recep Tayyip Erdogan, is cutting short an official visit to Latin America to return to Turkey.
11:03am: The Palestinian Ma'an News Agency is reporting (in Arabic) clashes between "Palestinian youths" and Israeli soldiers in Jerusalem's Old City; one soldier was lightly wounded in the fighting, according to Ma'an. Shopkeepers in the Old City are reportedly closing their businesses in protest of the Israeli attack on the flotilla.
There have also been other scattered demonstrations throughout the West Bank, including one in Nablus, according to Palestinian media reports.
10:59am: Al Jazeera's Sherine Tadros, reporting from Ashdod, just tweeted that a second boat from the flotilla is approaching the port (the first one arrived about an hour ago).
10:57am: Israel's National Security Counter-Terrorism Bureau just issued a travel warning for Turkey, warning of the threat of "violent outbreaks" against Israeli citizens traveling there.
It advises Israelis to postpone any trips to Turkey; for Israelis currently in Turkey, it recommends that they "should remain in their places of residence, avoid city centers and sites in which demonstrations are being held, and monitor developments out of concern that the situation could worsen."
10:53am: Sheikh Hamad bin Khalifa al-Thani, the emir of Qatar, was one of the first Arab leaders to condemn the attack; he called it an "act of piracy" in a speech earlier this morning.
Before I conclude I must briefly refer to what happened this morning: The Israeli act of piracy against Arab and foreign activists, who tried to break a non-humanitarian, unjust siege imposed on our fellow citizens in the Gaza Strip, [imposed] for no reason but [that] they exercised their democratic right of choice. The crimes perpetrated this morning against the civilians supporting the Palestinians remind us of the unjust siege, the open bleeding wound in the [Gaza] Strip. All those who preach freedom, justice and democracy are required now to move, and to act to break this siege, so the blood of these free men does not go down the drain. This is a message addressed to the Arab states, who were brought to the moment of justice by those free men on board."
Turkey's deputy prime minister announced a few moments ago that Turkey, too, is canceling joint drills with Israel.
10:43am: We're still trying to track down information about today's victims (various reports now put the death toll between 16 and 20).
We do know that the majority of the people on board the ships were Turkish. The passengers also include people from Algeria, Australia, Belgium, Canada, Germany, Greece, Ireland, Kuwait, Malaysia, Norway, Palestine, Serbia, Sweden, the United Kingdom, and the United States.
At least three of the German passengers were members of parliament.
10:32am: The Egyptian foreign ministry issued a statement condemning the flotilla attack, according to Al Jazeera's Amr El-Kahky, who sends this note from Cairo summarizing the statement.
The spokesman sent his condolences for the families of the victims. He added that such actions remind the world that Gaza is still entirely under occupation calling for the immediate lifting of the blockade. He vowed that Egypt will continue to ease the suffering of Gazans by allowing more individual passage to and from the coastal strip and making sure aid heading for Gaza is delivered to the beseiged Palestinians.
The Egyptian government temporarily opened the Rafah border crossing with Gaza earlier this month, but it generally maintains tight controls over the movement of people and goods.
Jordan's government is expected to issue a formal statement in about a half-hour.
10:10am: We're hearing from Iraq that Moqtada al-Sadr has called for a large anti-Israel rally across from the Green Zone in Baghdad. The rally is scheduled to start around 5pm local time (2pm GMT).
10:04am: Raed Salah, a senior member of the Islamic Movement in Israel, was reportedly seriously wounded during the attack, and is being treated in a hospital in Israel.
9:53am: More international condemnation continues to roll in:
Pakistan's foreign ministry issued a statement that "strongly condemns the use of brazen force by Israel."
The Jordanian foreign ministry has summoned the Israeli charge d'affaires, the ranking official at the Israeli embassy in Amman.
Saeb Erekat, the chief negotiator from the Palestinian Authority, called the Israeli attack "a war crime."
9:14am: The Stop the War Coalition and several other organisations are planning a rally this afternoon at 2pm local time (1pm GMT) outside the UK prime minister's residence.
8:59am: I just spoke with Greta Berlin, one of the flotilla's organisers, who said her organisation (the Free Gaza Movement) has had no contact with the passengers and crew on board the ships since they were attacked.
Berlin also strongly rejected the Israel's claim that the activists were the first ones to start shooting. She said there were no weapons on board the boats, and that any violence from the activists would have been in self-defense:
People certainly have the right to resist if they're being attacked. We taught our Free Gaza Movement people to be non-violent, and the Turks did the same, but if anyone resisted, it was in response to soldiers opening fire on them when they hit the deck.
Berlin also said organisers are still hoping to launch a second flotilla of boats, most of which remain at port in Cyprus.
We need to find out where the passengers are, where the crews are... and then we need to assess - we split up our flotilla, we have a second set of boats.
But Berlin said she didn't know when that second launch would happen; she expects it will be several days until everyone on board the first flotilla is accounted for.
8:43am: A statement from Saad Hariri, the Lebanese prime minister, who called the attack "dangerous and crazy":
The Israeli attack on the aid convoy is a dangerous and crazy step that will exacerbate tensions in the region.
Lebanon firmly denounces this attack and calls on the international community, notably major powers... to take action in order to end this continued violation of human rights and threat to international peace.
8:31am: Spain's foreign ministry has also summoned the Israeli ambassador for questioning. And Bernard Kouchner, the French foreign minister, described himself as "profoundly shocked" over the attack.
8:24am: An observation: We've heard a lot from the Israeli army, the Palestinian Authority, Hamas, the European Union, and a number of other governments.
The one party we haven't heard from in the last few hours is the organisers of the flotilla. Obviously it's impossible to reach those activists who were on board; and I haven't been able to reach their on-shore counterparts. The group's Web site hasn't been updated in the last few hours.
8:17am: This video, a report from Iran's state-run English-language Press TV network, shows a large crowd of protesters gathered outside the Israeli consulate in Istanbul this morning.
8:05am: Turkish media are reporting protests throughout the country, particularly in Istanbul (several of the ships, and many of the activists on board, are Turkish). 300 people tried to storm the Turkish consulate in Istanbul early this morning; a larger protest is planned for 12:30 local time (9:30GMT).
"Massive" security is reported around the Israeli embassy in Ankara, and around the residence of Gaby Levy, the Israeli ambassador.
There are also reports of a small demonstration outside the US consulate in Adana, a city in southern Turkey.
7:53am: A few more international reactions:
The European Union has called for an inquiry into the attack. Individual European governments are also starting to issue statements: Sweden's foreign minister, Carl Bildt, said his government summoned the Israeli ambassador "to get information."
The Syrian government has called for an Arab League meeting to discuss the attack.
Kuwait's parliament is due to hold an emergency meeting today to discuss the raid. Waleed al-Tabtabai, a member of parliament, was one of 16 Kuwaiti nationals on board the ships.
7:47am: We're getting reports of a protest planned for later this morning outside the prime minister's office in Amman, Jordan. The organisers are reportedly demanding the closure of the Israeli embassy in Amman.
7:39am: If you haven't seen it, here's the report our Jamal Elshayyal filed shortly before communications from the ships were cut off.
7:21am: Israeli prime minister Binyamin Netanyahu is scheduled to visit Washington later this week to visit US president Barack Obama. Ha'aretz reports that he may cancel the trip in the wake of the flotilla attack (though we should note the Ha'aretz report isn't actually sourced to anyone).
7:11am: Avital Leibovich, a spokeswoman for the Israeli military, is giving a press conference right now at Ashdod port, where the navy originally planned to tow the flotilla ships after seizing them.
Leibovich acknowledged that the flotilla was seized in international waters, not in Israeli territorial waters.
During the intercept of the ships, the demonstrators onboard attacked the IDF Naval personnel with live fire and light weaponry including knives and clubs. Additionally one of the weapons used was grabbed from an IDF soldier. The demonstrators had clearly prepared their weapons in advance for this specific purpose.
As a result of this life-threatening and violent activity, naval forces employed riot dispersal means, including live fire.
The Israeli foreign ministry is expected to comment on the attack within the hour.
7:07am: Over in the West Bank, Palestinian president Mahmoud Abbas declared a three-day state of mourning over the flotilla deaths. He also issued a brief statement:
Palestinian President Mahmoud Abbas condemns the crime perpetrated by the occupation authorities against international solidarity activists aboard the Freedom Flotilla. The Palestinian leadership is closely following the developments and the President calls on the United Nations to confront Israel, which is disregarding all international laws and norms.
The Palestinian cabinet is scheduled to convene about one hour from now, at 8am GMT.
6:58am: Ismail Haniya, the Hamas leader in Gaza, wrapped up a speech to journalists a few minutes ago. He called on the Palestinian Authority to end its indirect talks with Israel, demanded a United Nations Security Council meeting to discuss the attack on the flotilla, and called for a general strike tomorrow (Tuesday) in the West Bank and Gaza.