The operational missions included flying supplies and personnel to Army units fighting the Japanese, evacuating wounded soldiers and conducting reconnaissance tasks.

The next day an Auster crashed while taking off from a newly constructed small airstrip within the Allied beachhead, resulting in the death of the aircraft's observer, an Army Air Liaison Officer, Lieutenant Stanley Ket.

16 AOP Flight detachment landed on Labuan island on 10 June, and subsequently supported the 9th Division throughout the Battle of North Borneo.

During late June aircraft from this detachment rescued eleven downed American airmen from a valley central Borneo.

16 AOP Flight flew air cover over HMAS Burdekin while the official surrender of Dutch Borneo was signed on board the ship on 10 September.

16 AOP Flight was ordered to cease flying operations on 6 November 1945, and it returned to Australia by sea later that month.

16 AOP Flight was occasionally used to support the Australian Capital Territory Police Force and conduct aerial photography for the Commonwealth Scientific and Industrial Research Organisation.

[7] In August 1960 it was announced that the flight would be expanded to squadron strength and also begin to operate Bell 47G Sioux helicopters.