Renumbered from 43 Squadron at Cairo West on 12 March 1944 with Ansons, the squadron began conversion to the Dakota by the end of the month. The squadron was involved in scheduled and unscheduled flights throughout the region and even as far as Rome, Russia, Karachi and the Gold Coast (Ghana). In February 1945 the squadron moved to the Italian port of Bari for operations in the Balkans, including providing support to Yugoslav partisans. The squadrons activities were not confined to the Balkans, with general transport and VIP flights to the south of France, Turkey, Egypt and Britain. The squadron was eventually disbanded at Bari on 6 December 1945.
The squadron was reformed in November 1953 at Swartkop as a transport unit flying Dakotas by renumbering 25 Squadron. The squadron spent a few years at Waterkloof between 1956 and 1963 before returning to Swartkop. Ex-SAA DC-4 Skymasters joining the fleet in 1966. The Vickers Viscount was transferred from 21 Squadron in October 1983 and flew with the squadron until sold in 1991. In 1992, the squadron moved to AFB Waterkloof and re-equipped with Dakotas converted to the C-47TP standard. The Skymasters were retired in 1994. During 1998 the C-47TPs were transfered to 35 Squadron when the squadron took over the CASA 212s and CN-235 of the disbanded 86 MEFS. With the disbanding of 42 Squadron in February 2000, 44 Squadron took over their Cessna 185's as well, using them to form B Flight, while the CASAs formed A Flight.
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