The officers could face life in prison if convicted in a Turkish court, Today's Zaman reported.
The 144-page indictment names Defense Forces Chief of General Staff Gabi Ashkenazi, Naval Forces commander Vice Adm. Eliezer Marom, Israel's military intelligence chief Maj. Gen. Amos Yadlin and Air Forces Intelligence head Brig. Gen. Avishai Levi as defendants.
In May 2010, the Israeli Navy attacked an international aid flotilla, killing eight Turkish nationals and one Turkish American who were trying to break an Israeli blockade of Gaza.
Turkey has called the attack a violation of international law "tantamount to banditry and piracy" and described the killings of activists as "state-sponsored terrorism."
Turkey said it was "surprised, appalled and dismayed that the national inquiry process in Israel has resulted in the exoneration of the Israeli armed forces."
Ankara has called for an official apology from Israel for the raid.
The trial of the military officers is set to begin in the Istanbul 7th High Criminal Court on Tuesday.