UN Secretary General Ban Ki-moon called on Israel to conduct a full investigation into the incident.
"I am shocked by reports of killings and injuries on boats carrying supplies for Gaza," he said. "I condemn this violence."
The UN’s rights chief Navi Pillay also said she was "shocked" after Israeli commandos stormed the Gaza-bound aid ship.
“We are in contact with Israeli authorities to express our deep concern and to seek a full explanation,” said a joint statement from Robert Serry, the UN Middle East envoy, and Filippo Grandi, head of the UN agency for Palestinian refugees.
In Europe there was a chorus of condemnation. French Foreign Minister Bernard Kouchner said he was “deeply shocked” by the attack, adding that “nothing can justify” such action.
Spain, which holds the current European Union presidency, called the Israeli ambassador to Madrid to explain what they called an “unacceptable” operation.
The 22-country Arab League also criticised Israel. Its chief Amr Moussa called the action a “crime” against a humanitarian mission, and urged everyone to condemn it. He said a meeting tomorrow would decide a “collective position”.
Lebanese militant group Hezbollah said the Israeli raid was a “crime against humanity”.
“This crime illustrates to the world Israel’s savagery and the way they deal with unarmed civilians,” Hezbollah MP Hassan Fadlallah told the AFP news agency.
Iranian President Mahmoud Ahmadinejad said Monday’s attack was an “insult to human dignity”.
“It is clearly evident that the Palestinian issue is not an Arab or Islamic one, but a world issue. Today, the reason for creating and imposing of the Zionist regime has become evident to all,” the hardliner told the official INRA news agency.
Arabs in Israel announced a one-day strike in protest against the attack. The Higher Arab Monitoring Committee said a strike would take place on Tuesday.