Technically, there was no "Japanese Air Force" in the modern sense of an independent service. Instead their were Air units in both the Imperial Japanese Army and Imperial Japanese Navy. (Although, The naval units were often land based, the IJN's Air arm was vastly larger than just it's carrier wing pilots.)

So did these Air Units engage in war crimes? Only "incidentally", since they mostly stayed on airfields and did their jobs. (Unless you consider bombing civilian targets and the kamikaze program war crimes.) Most war crimes were committed by Military Police/Shore Patrol units or Infantry units assigned to attack cities, which existed in both the Army and Navy. Strafing parachuted pilots was widely reported, but is not normally thought of as a war crime, and was done by both sides.

All that being said, they were still part of the Japanese military and shared its culture, in which brutal treatment of civilians and prisoners was rather widespread. They were just less likely to encounter them.