On 16 July 1943 the Fort Longueuil left Barry docks with a cargo of government stores, including ammunitions and arrived safely at Alexandria on 8 August. After the cargo was discharged she sailed from there on 26 August, sailing through the Suez Canal two days later and docked at Aden on 8 September to bunker. The next day, the ship left for Australia after loading phosphate. She was due to arrive at Fremantle, Australia and then to sail to Port Kembla and Newcastle, New South Wales, but was reported missing on 15 October. By 3 November, it was known that the ship had been lost at the estimated position of 10°S/68°E.

On 19 Sep 1943 the unescorted Fort Longueuil (Master George Cardno Edward) was torpedoed by U-532 and sank immediately southwest of Chagos Archipelago. The complement consisted of 49 crew members from Britain, India and Canada and ten British gunners (the ship was armed with one 4in and five 20mm guns). Only two Indian crewmen, Thakar Miah and Mohamed Aftab, managed to survive on a raft and became Japanese prisoners on 1 Feb 1944, when the raft drifted ashore on Sumatra after 134 days at sea (!).