Foreign Minister Ahmet Davutoglu accused Israel of wasting Turkey's efforts to normalize relations, Today's Zaman reported Friday.
Nine people died when Israeli soldiers boarded the Mavi Marmara as it tried to break the blockade of Gaza last year.
Israel said it regretted the loss of life but would not apologize.
"Israel, like any other country, has the legitimate right to defend its citizens and soldiers," an Israeli official told the BBC. "The state of Israel hopes a way will be found to overcome the disagreements, and will continue to work to achieve this goal.
Israeli soldiers, the official said, were attacked with batons, knives and steel pipes.
"During the events of the Mavi Marmara flotilla, Israeli soldiers boarded the boat with non-lethal means. They had no intention to hurt anyone," the official said.
Today's Zaman said officials are angered by information in the leaked U.N. report on the incident, in which nine Turkish civilians were killed while delivering humanitarian aid to Gaza in breach of an Israeli naval blockade.
Turkey has demanded an official apology and compensation for the families of victims.
Davutoglu said Turkey is expelling Israel's ambassador to Turkey and suspending all military agreements with Israel. He said the country will seek a review of the Israeli blockade of Gaza by the International Court of Justice.
The U.N. report on the flotilla, obtained and published Thursday by The New York Times, said Israeli commandos acted in self-defense but criticized the soldiers for using "excessive and unreasonable" force.