Turkish Prime Minister Tayyip Recep Erdogan said the incident represented a complete violation of international law.
"This action, totally contrary to the principles of international law, is inhumane state terrorism. Nobody should think we will keep quiet in the face of this," Erdogan told reporters from Chile, where he was cutting short an official visit to Latin America to deal with the crisis.
Turkey and Israel hold diplomatic ties, though they have been strained over the last year.
Egypt, which in 1979 became the first Arab state to sign a peace treaty with Jerusalem, summoned Israel's envoy in Cairo in response to the incident.
The Arab League, meanwhile, urged member states to "reconsider" their dealings with Israel. Syria asked for an emergency Arab League meeting to discuss what it described as Israeli aggression on Gaza-bound international aid ships.
"Syria's representative to the Arab league has submitted a formal memo to the League requesting it to convene," the official Syrian news agency said.
"Israel's attack indicates Israel is not ready for peace. Israel attacked the liberty fleet because it feels it is above the law," Arab League Secretary General Amr Moussa said in Doha.
"There is no benefit in dealing with Israel in this manner and we must re-assess our dealing with Israel," he said.
Israeli commandos intercepted the aid flotilla on Monday. Officials said they were met with knives and staves when they boarded the ships, which included a ferry flying the Turkish flag.
Israel's foreign ministry warned its citizens to avoid travel to Turkey and instructed those already there to keep a low profile and avoid crowded downtown areas.
Turkey denounced Israel's killing of 10 left-wing activists as "unacceptable" and summoning Israel's ambassador to discuss the incident - bringing already tense relations between the countries to new heights.
The ministry said that Israel had violated international law and must now carry the consequences."The interception on the convoy] is unacceptable ... Israel will have to endure the consequences of this behavior," it said in a statement.
Murat Mercan, a lawmaker from Prime Minister Recep Tayyip Erdogan's ruling party, said: "I was expecting an intervention. I was not expecting bloodshed, the use of arms and bullets."
"Israel is engaged in activity that will extremely hurt its image," he said. Erdogan, meanwhile, cut short a trip abroad to deal with the incident.
Palestinian President Mahmoud Abbas described the clashes as a "massacre".
Iran said the killings were "inhuman" and would help lead to Israel's demise, and some 200 Iranians staged a demonstration near the United Nations building in Tehran to protest against the storming.
"All these acts indicate the end of the heinous and fake regime and will bring it closer to the end of its existence," President Mahmoud Ahmadinejad told state broadcaster IRIB. Iran is under international pressure over its nuclear program.
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