The plane was denied permission to cross Turkish airspace and was therefore forced to fly an alternative route.
Meanwhile, Israel's commission of inquiry into the flotilla raid opened on Monday.
The official said this particular flight was banned purely because it had been the first such request from Israel and had nothing to do with the nature of the flight.
Civilian flights are unaffected.
Reports first surfaced in the Israeli newspaper Yediot Ahronot that an Israeli military cargo plane, carrying more than 100 officers on their way to Auschwitz, was barred from Turkish airspace.