Following the state funeral service for the victims, the Istanbul-Bakırköy prosecutor’s office opened a criminal investigation into the acts of piracy committed in the Mediterranean on 31 May 2010.

Prosecutor Mehmet Tastan ordered an autopsy to be performed on the nine corpses returned by Israel. It appears that nearly all were killed with bullets fired at close range.

He also arranged for the hearing of witnesses and victims (except for those who are in hospital under intensive care).

According to well-informed sources, the prosecutor is contemplating the conviction of pirate chiefs Benjamin Netanyahu (Israeli Prime Minister), General Ehud Barak (Defence Minister) and General Gabi Ashkenasi (Chief of Joint Staff). They are expected to be charged with piracy, assault, murder, kidnapping and arbitrary imprisonment. The prosecutor should confine his conclusions to the crimes committed against Turkish nationals aboard the two ships flying the Turkish flag. He may also file charges for crimes against humanity under Article 77 of the Turkish Penal Code.

The Department of Justice has set up a working group to examine all the implications of this case both in terms of national and international law. In the event a Turkish court were to condemn Israeli citizens in absentia and that Israel obstructed the execution of sentence, the plaintiffs may forego their rights in favour of the Turkish state, which could then refer the case to the United Nations.

The Justice Committee of the Turkish Parliament has already seized its counterparts at the EU Parliament and the Council of Europe Parliamentary Assembly.

Moreover, the death of 19 year-old Furkan Doğan, a dual U.S.-Turkish national, has put the U.S. State Department in a quandary. While the Obama administration has countered so far a Security Council investigation commission, pledging its confidence in Israeli Justice to conduct a "prompt, impartial, credible and transparent investigation conforming to international standards", it may prove more difficult for it to prevent the opening of a criminal trial by a U.S. court.