Following the Japanese surrender ceremony in Tokyo Bay, No. 16 AOP Flight flew air cover over while the official surrender of Dutch Borneo was signed on board the ship on 10 September. Other Austers from the flight escorted a Japanese aircraft to Labuan. No. 16 AOP Flight was ordered to cease flying operations on 6 November 1945, and it returned to Australia by sea later that month. A nucleus from the flight arrived at RAAF Station Canberra on 3 December, and flying operations resumed there on 3 January 1946. No. 16 AOP Flight was disbanded on 23 June 1947.