While Israel's diplomats worked to calm international outrage, its navy said it was ready to intercept another aid vessel that organisers of the flotilla planned to dispatch to the Gaza Strip, an enclave run by Hamas Islamists, next week.
Big questions were unanswered: how far Israel could continue to blockade 1.5 million Palestinians in the Gaza Strip after condemnation from allies, and how it misjudged the situation and dropped marines yesterday onto a Turkish ship where they felt they had to open fire to save their lives.
Activists were held incommunicado by Israel but their accounts began to emerge after some were deported.
"We did not resist at all, we couldn't even if we had wanted to. What could we have done against the commandos who climbed aboard?" said Mihalis Grigoropoulos, who was aboard a vessel behind the Mavi Marmara, the cruise ship on which most of the violence occurred.
"The only thing some people tried was to delay them from getting to the bridge, forming a human shield. They were fired upon with plastic bullets and were stunned with electric devices," Grigoropoulos told NET TV at Athens airport.
Video: UN urges Israel probe
Prime Minister Benjamin Netanyahu, who returned from Canada after cancelling White House talks that had been planned for today, was to convene his cabinet to discuss the fallout from what Israeli newspapers termed a blundered operation.
US President Barack Obama, who has succeeded in reviving Israeli-Palestinian peace negotiations through US-mediated indirect talks, said he wanted the full facts soon and regretted the loss of life.
Turkish Prime Minister Tayyip Erdogan urged Israel to lift what he called its "inhumane embargo" of Gaza as soon as possible. Once-close Muslim ally Turkey has described Israel's storming of the ships as "state terrorism".
After more than 10 hours of closed-door talks that gave rise to conflicting interpretations, the UN Security Council called for "a prompt, impartial, credible and transparent investigation conforming to international standards".
It also condemned "those acts which resulted in the loss of at least 10 civilians and many wounded". Earlier Israeli reports had put the death toll at 10.
The use of the word "acts" instead of "act" - the term preferred by Turkey - suggested that activists who attacked the Israeli boarding party also bore some responsibility.
Alleging bias, Israel refused to cooperate with the UN Goldstone commission's inquiry into a Gaza war that it launched in December 2008 with the declared aim of ending cross-border rocket fire.
The inquiry found evidence that both Israel and Palestinian militants had committed war crimes, but the report was harsher toward Israel.
Some 700 activists were processed in and around Israel's port of Ashdod, where the six ships of the blockade-running convoy had been escorted. Among the activists were many Turks but they also included Israelis and Palestinians as well as Americans and many Europeans - among them politicians - a Jewish Holocaust survivor and Swedish author.
The military said the nine activists were killed when commandos, who stormed the Mavi Marmara from dinghies and helicopters, opened fire in what Netanyahu said was self-defence.
The Interior Ministry said today that 50 activists had been taken to Ben-Gurion Airport for voluntary repatriation. Around 629 had refused, and would be held while Israel weighed its legal options. Some 30 were in hospitals with injuries.
Adding his criticism of Israel's actions, Russian President Dmitry Medvedev said the loss of life was "irreparable and absolutely unjustified".
British Prime Minister David Cameron spoke to Netanyahu by telephone late yesterday and "deplored the heavy loss of life off the coast of Gaza", a spokesman for the British leader said.
Cameron "also stressed the importance of urgently lifting the blockade of Gaza, and allowing full access for humanitarian aid". Israel says it transfers large amounts of aid to the territory daily and that there is no humanitarian crisis there.
Video: Gaza aid ships violence condemned
Israeli Internal Security Minister Yitzhak Aharonovitch said police were gathering evidence to prosecute activists who had set upon the marines with fists, batons, knives and gunfire.
"All those who lifted a hand against a soldier will be punished to the full extent of the law," he told Israel Radio.
The European Union, a main aid donor to the Palestinians, and Russia demanded an inquiry and an end to the embargo. Netanyahu voiced regret at the deaths but vowed to maintain the blockade to stop arms smuggling by Iranian-backed Hamas.
Western-backed Palestinian President Mahmoud Abbas - no friend of Hamas which seized the Gaza Strip from his Fatah faction in 2007 - called the Israeli operation a "massacre".
