In 1965, Air-Mshl. Khan reportedly was in conflict with the army department led by its army commander General Musa Khan when he questioned the contingency plans and secret infiltration into the Indian held side of Kashmir. Air-Mshl. Khan reported that neither the Air Force nor the Pakistan Navy was kept informed by military planners when the Indo-Pakistani War of 1965 (the second war with India) broke out. Before the declaration of war by either side, Air-Mshl. Khan reportedly spoke with Air-Mshl. Arjan Singh, the Indian Air Force's Chief of the Air Staff, where both reached a mutual understanding for avoiding bombardment of each sides residential cities.