Yes, General Masaharu Honma, who was in charge of the troops, was executed in Manila after the war after being convicted of war crimes.
War crimes were in fact the criminal offence that was already well established, and it was crimes against humanity and especially crimes against peace that were more novel and problematic.
As already stated, General Homma was tried and found guilty of crimes against humanity (huh would have thought war crimes covered it) based on his being the commander of the Japanese forces and having failed to stop the actions of his troops.
More generally, several of the defendants before the IMTFE were charged with mistreatment of POWs, including those in the Philippines, and found guilty based on command responsibility.