The report does not fault the commandos who opened fire after being confronted by violent pro-Palestinian activists on board one of the ships. Eight Turks and one Turkish-American died in the May 31 raid.
Declassified sections of the report released Monday say faulty intelligence led the military to underestimate the potential for violent resistance on board.
The incident occurred on board the Turkish ship Mavi Marmara, which was intercepted by helicopter-borne Israeli commandos as it sailed in a six-ship flotilla carrying pro-Palestinian activists and supplies to the Gaza Strip.
Five ships were commandeered without incident, but some of the 600 activists on board the Mavi Marmara, owned by a Turkish Islamic charity, actively resisted, and the soldiers opened fire.
The soldiers, seven of whom were wounded, said their lives were in danger. Activists called their actions self-defense.
Although Israel has said the blockade is necessary to keep weapons out of the hands of Hamas, it has come under heavy international criticism over the raid.