[4] The squadron was re-equipped with Lockheed Hudson light bombers, suffering its first loss in September when an aircraft was destroyed on take-off.

[2] In May 1941, the squadron began familiarisation flights over the Netherlands East Indies in preparation for deploying to the NEI following the outbreak of war with Japan.

13 Squadron deployed two flights of Hudsons (a total of six aircraft) to Ambon, where they were based at Laha Airfield in the NEI.

The remainder of the Aircraft were left at Darwin pending the executive from higher authority to proceed to Namlea, NEI.

[12] Nevertheless, the squadron continued to fly operational attack and reconnaissance missions over the NEI, including an anti-shipping raid around Beco, in Timor, on 10 August 1942, sinking Japanese netlayer Fukuei Maru No.

15 and damaged another in a mast-height attack that was launched in response from intelligence information provided by Australian commandos deployed on the island as part of Sparrow Force.

At Fairbairn the squadron took delivery of Bristol Beaufort and Lockheed Ventura aircraft and conducted anti-submarine and shipping patrols along the Australian east coast.

[11][14] The future Australian Prime Minister Gough Whitlam served with the squadron as a navigator from 2 August 1943 until February 1945.

[4] In late June 1945, the squadron moved to Morotai in the NEI and, soon after the end of the war, to Labuan in British North Borneo.

From Labuan the squadron operated in the transport role and ferried ex-prisoners of war and other personnel back to Australia before being disbanded on 11 January 1946.