No. 42 Squadron commenced minelaying operations in September 1944, laying mines off Celebes. Here it suffered its first loss on 23 September when a Catalina made a forced landing in Japanese-controlled territory; the aircraft's crew were later rescued by a No. 43 Squadron Catalina. The squadron focused on laying mines off Makassar and Pare Pare Bay in Celebes during October, and lost two aircraft to Japanese anti-aircraft guns. In November a detachment of aircraft was deployed to Morotai in the NEI, which had been captured by Allied forces in mid-September. From here, they flew minelaying operations against Brunei Bay, Tarakan, Sandakan, and the Balabac Straits. Later in 1944, seven No. 42 Squadron Catalinas were deployed to Leyte in the Philippines from where they mined Manila Bay on the night of 14/15 December.