Personnel began marching in and by the end of the month, the squadron's strength had reached 17 officers and 394 other ranks.

The squadron was still in the process of concentrating in Darwin when the war ended in August, with the move finally being completed in late September.

99 Squadron operated in the transport role and was responsible for flying personnel and supplies between Darwin and southern Australia.

The squadron suffered its first loss on 14 September when a Liberator crashed near RAAF Base Amberley, killing five crew members.

99 Squadron moved from Darwin to Tocumwal, New South Wales, where, the following month, further losses were incurred when one member was killed and four injured in a vehicle accident on the ground.