Turkey's top prosecutor sent a letter to Israeli officials asking for the identities of both the soldiers who stormed the Turkish flagged Mavi Marmana and the political and military leaders involved in the operation, according to the Zaman newspaper.
The letter was transmitted through Turkey's justice and foreign ministries, the paper said.
The request is part of Turkey's ongoing investigation for premeditated murder, which has already implicated Israeli President Shimon Peres, Prime Minister Benjamin Netanyahu, defence minister Ehud Barak and foreign minister Avigdor Lieberman.
The Mavi Marmana, dispatched by the Turkish humanitarian organisation IHH was stormed by Israeli forces on May 31 in international waters as it approached Gaza, hoping to breach a blockade on the area imposed by Israel.
Nine Turkish nationals were killed in the operation, including one person who also had US citizenship.
Israel's action provoked widespread international condemnation and Turkish President Abdullah Gul said bilateral relations between the two countries "would never be the same again."
In January, an Israeli inquiry ruled that the raid was in keeping with international law.
Ankara said it was "stunned and dismayed" by the finding.
Another aid convoy, which includes the Mavi Marmana, is expected to set out for Gaza in late June.
Last month Israel expressed concern over the planned mission, calling it an "incitement to violence."