Turkey, which currently holds a rotating seat on the U.N. Security Council, demanded it meet about the killings, which Prime Minister Bulent Arinc equated with "piracy." He denied Israeli statements that some on the ships headed for the Gaza Strip were armed and had attacked the Israeli soldiers.
The raid was a devastating blow to relations between the long-time allies, already deeply strained by tensions over Israeli actions in Gaza. Prime Minister Recep Tayyip Erdogan was cutting short his Latin America tour and was expected to return home on Tuesday.
Arinc said, however, that there would be no immediate action on the country's defense cooperation with Israel.
Three of the ships were Turkish-flagged, including the main passenger ship, and the convoy was led a pro-Islamic Turkish aid group. Arinc said about 400 out of 581 passengers on the main ship, the Mavi Marmara, were Turks
"I strongly condemn the use of force by Israeli military forces on an aid convoy composed of 32 countries, including Turkey," he said. "This attack must not remain unanswered.
"We are calling our ambassador today," he said. "We have also canceled three military drills with Israel as well as calling back our under-18 soccer team from Israel."
He ruled out deploying Turkish warships in the Mediterranean. Two of the cancelled military drills were search and rescue exercises in the Mediterranean and the third was a drill in Israel later this year.
He insisted that the Turkish government was not involved in the organization of the flotilla, saying it was a pure act of nongovernmental organizations.
But he disputed reports that the Israelis only opened fire after being attacked by activists with sticks, knives and live fire from weapons seized from the Israeli commandos.
"Israel might be trying to defend itself or justify its action," Arinc said. "What we know is that the ships were totally unarmed and set sail for humanitarian purposes."