As the Islamist Hamas which rules in Gaza urged world Muslims to "rise up" in protest, police struggled to hold back an angry crowd of hundreds outside the Israeli consulate in Turkey's biggest city Istanbul.
Furious protesters shouted "Damn Israel" outside the residence of Israel's ambassador to Ankara, who was summoned for immediate talks as Turkey warned of "irreparable consequences" to bilateral ties.
"This deplorable incident, which took place in open seas and constitutes a fragrant breach of international law, may lead to irreparable consequences in our bilateral relations," a written statement said.
"By targeting civilians, Israel has once again shown its disregard for human life and peaceful initiatives," Ankara said.
Israel claimed its naval forces were attacked by activists and that both sides used live fire, after they stormed six ships bound for besieged Gaza with thousands of tonnes of aid and hundreds of pro-Palestinian activists aboard.
But Iran's President Mahmoud Ahmadinejad denounced the raid as "inhuman Zionist regime action."
Palestinian president Mahmud Abbas declared three days of mourning over the "massacre," while the Arab League chief Amr Mussa called it a "crime" and said the 22-country body was consulting on its next step.
Kuwait's parliament speaker condemned the storming of the flotilla, which was carrying 16 Kuwaitis including an MP, as a "heinous Israeli crime."
In Europe, condemnation was equally swift.
The European Union demanded Israel mount a "full inquiry," with foreign affairs chief Catherine Ashton demanding "an immediate, sustained and unconditional opening" of crossings to Gaza.
Spain -- the current European Union president -- Sweden and Greece summoned the Israeli ambassadors to their capitals to demand explanations, with Madrid slamming the operation as "unacceptable".
Greece, which had some 30 nationals on board the flotilla, also withdrew from joint military exercises with Israel in protest at the raid.
French Foreign Minister Bernard Kouchner said he was "deeply shocked" by the Israeli raid and insisted "nothing can justify" such violence.
Germany's Foreign Minister Guido Westerwelle also said he was "deeply concerned" about the deaths.
The bloody ending to the high-profile mission to deliver supplies to Gaza came on the eve of a meeting in Washington between President Barack Obama and Israeli Prime Minister Benjamin Netanyahu.
Maen Bashur, a Lebanese activist and coordinator for a group called End the Blockade on Gaza, said they had expected the convoy to be "attacked" by the Israelis and considered those seized on board the ship as "war prisoners".
"For that reason we asked Hezbollah's leadership to act accordingly," Bashur said.
When asked whether he was encouraging the Shiite militant group to launch a cross-border raid and seize Israeli hostages, Bashur responded: "Hezbollah's leadership is wise and knows how to behave."
A Cyprus MEP Kyriacos Triantafyllides, who was prevented at the last minute from joining the aid mission, told the Cypriot news agency CNA that activists had "expected a strong reaction from Israel."
"But nobody believed it would come to this point where they would face something akin to an invading army," he said.
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