Raised in early 1943, the squadron flew Catalina aircraft from bases in Queensland and the Northern Territory, flying mine-laying, convoy-protection and bombing sorties against Japanese targets in the Pacific theatre.

43 Squadron was formed at Bowen in Queensland on 1 May 1943, initially under the command of Flight Lieutenant I.L.

[2] As well as flying convoy protection and anti-submarine patrols along the Australian east coast the squadron conducted offensive operations against Japanese shipping in the Solomon Islands and the eastern islands of the Netherlands East Indies,[3] with a detachment maintained at Bowen during this time.

43 Squadron conducted mine laying operations throughout South East Asia, venturing as far as the Philippines, Hong Kong and the Chinese coast.

[4] The squadron also undertook air-sea rescue operations, supporting long-range Allied bombing missions in the Netherlands East Indies from early 1944.

43 Squadron Catalinas shadowed the Japanese cruiser Isuzu, which was subsequently sunk by Allied bombers and submarines.

43 Squadron performed routine patrol and transport flights until moving to RAAF Base Rathmines in November 1945.