Ex-military chief of staff Gabi Ashkenazi and former heads of military intelligence, the navy and air force are expected to be tried in absentia.
The nine pro-Palestinian activists were killed after Israeli troops boarded their ship, the Mavi Marmara.
They had been hoping to breach Israel's naval blockade and deliver aid to Gaza.
A prosecutor at the court in Istanbul has called for each of the four Israeli officers to face nine life sentences, Turkish news agency Anatolia reported.
The other three commanders are ex-naval chief Vice Admiral Eliezer Marom, former head of military intelligence Major General Amos Yadlin, and former head of the air force Brigadier General Avishai Lev.