The squadron was one of only a few RAAF airfield construction units to be retained at the end of the war, and formed part of Australia's contribution to the occupation of Japan from 1945 until it was disbanded in June 1949.

[6] In order to support Allied offensives in New Guinea 5MWS moved to Goodenough Island between late February and March 1943 where it constructed Vivigani Airfield.

[8] In early 1944 5MWS became part of a force of RAAF and United States Army aviation engineer units which were selected to build airfields at Aitape in New Guinea from which air support would be provided to Allied operations around Hollandia after US Army forces landed there on 22 April.

5MWS departed Melbourne on 15 February, and eventually joined up with the main body of the airfield engineer force at Lae on 1 April where it received training in infantry tactics.

[12] The two squadrons landed at Labuan on 11 June and worked on repairing and maintaining the island's airfield until the end of the war on 15 August.

[13][14] While most of the RAAF's airfield construction squadrons were disbanded at the end of the war, on 17 November 1945 5ACS was informed that it would form part of Australia's contribution to the British Commonwealth Occupation Force (BCOF) in Japan.

At this time the unit was under strength as only 14 officers and 189 airmen had volunteered for occupation duties, though a further 173 personnel arrived in March and April.

[13][19] 5ACS was reformed on 8 August 1951 at Bankstown, New South Wales to fill the RAAF's need for engineering units and provide a nucleus for the potential formation of other airfield construction squadrons.

[20] Between March and November 1952 a detachment of 30 men from 5ACS was deployed to the Montebello Islands off the coast of Western Australia to support the British nuclear weapons test in the area, Operation Hurricane.

[13] Most of 5ACS moved to Darwin in 1955 to build a 13,000-foot (4,000 m)-long runway and supporting facilities at RAAF Base Darwin, though a detachment remained at Williamtown until June 1963 and two other detachments were formed to undertake engineering tasks in the Sydney region and rebuild the runway at RAAF Base Amberley.

For a short period the remnants of 2ACS was designated Detachment C of 5ACS while it completed works on RAAF Base East Sale; this sub-unit was disbanded in September 1961.

[24] RAAF units began to be deployed to South Vietnam in 1964, and in May 1966 Detachment A of 5ACS was formed at Vũng Tàu to improve the airfield there so it could support the UH-1 Iroquois-equipped No.

Initial works began on this project in March 1970 when Detachment E of 5ACS was formed there, and the main body of the squadron arrived on 1 February 1971.

5ACS' task was to extend the existing runway at the site and build facilities to support RAAF combat aircraft in the case of a war with Indonesia.

Nonetheless, the runway and extensive support facilities were officially opened on 15 December 1972, though further work needed to be completed at this time.

The squadron's strength declined during 1974 as personnel left the RAAF or moved to other units, and it was disbanded at Learmonth on 15 December 1974.

[27] 5ACS was the last of the RAAF's airfield construction units, and since its disbandment civilian contractors have been used to build and maintain air bases.

65 Squadron was raised to centralise the RAAF's airfield repair and recovery capabilities: the '5' in its title was selected in recognition of 5ACS.