"It appeared to pose a real threat and was fired at," the military said in a statement, without specifying the type of the aircraft.
The military called it a "serious incident" and promised that the lesson would be learned.
Israeli media published conflicting reports on which aircraft it was. The Times of Israel identified it as a crop-duster, while the Yedioth Ahronoth daily said it was doing aerial photography.
The plane was reportedly hit by bullets but no one was hurt. The pilot was cited as saying he thought it was a bird strike before noticing a drop in fuel pressure.