A UN inquiry into the Israeli commando raid on the aid convoy on May 31 was due to meet for the first time later in the day. The killing of the activists, all Turks, although one was a US citizen, almost caused a breakdown in relations between the Jewish state and its once close ally.
"No one else can take the blame for killing civilians in international waters," Davutoglu told journalists.
"Israel has killed civilians, and should take the responsibility for having done so."
The Turkish minister appeared to be responding to comments by Prime Minister Benjamin Netanyahu on Monday to a separate Israeli inquiry into the fatal raid.
Netanyahu said Turkey had ignored repeated warnings and appeals "at the highest level" to halt the flotilla, which was organized by an Islamic charity based in Turkey.
"Turkey has no responsibility in the attack on the Mavi Marmara flotilla," Davutoglu said.
On Tuesday, Defense Minister Ehud Barak told the Israeli panel that Israel had exhausted all other options before carrying out the raid.
Turkey withdrew its ambassador after the raid and called off joint military exercises, but stopped short of breaking diplomatic ties completely. It wants Israel to apologize and offer compensation to the victims' families.
Israel says its commandos opened fire after activists attacked a boarding party with clubs and knives.
Relations between Turkey and Israel began deteriorating after Prime Minister Tayyip Erdogan condemned an Israeli offensive in Gaza in December, 2008, and criticized an Israeli blockade of the Palestinian enclave.
Israel said the blockade was necessary to stop arms reaching the Islamist Hamas group running Gaza. After an international outcry over the raid on the aid convoy, Israel relaxed the embargo.
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