This came as the UN published a report saying that Israeli commandos used excessive force when they boarded an aid ship. Nine Turkish activists died.
Turkish Foreign Minister Ahmet Davutoglu said it was "time Israel pays a price for its illegal actions".
Israel has refused to apologise and said its troops acted in self-defence.
"Israel, like any other country, has a legitimate right to protect its citizens and soldiers," an Israeli government official told the BBC.
"Israel has made many attempts in the recent months to settle the dispute between our countries. Unfortunately these attempts were unsuccessful."
The report was leaked to the New York Times on Thursday, the day before it was delivered to UN Secretary General Ban Ki-moon's office.