The only operational RAAF squadron to use the Lockheed Ventura in Australia and the SWPA was No 13 Squadron. (No 459 Squadron and No 464 Squadron operated RAF Venturas in the Middle East and U.K. respectively). Formed at Darwin on 1st June 1940 with Avro Ansons, No 13 Squadron re-equipped with Lockheed Hudsons the same month. In anticipation of hostilities with Japan, Hudsons were detached to Laha and Namlea in the Netherlands East Indies. After incurring heavy losses, the Squadron consolidated at Darwin from where reconnaissance flights and bombing missions continued. Enemy air raids on Darwin prompted a partial withdrawal south to Daly Waters in February 1942 and again to Hughes in May 1942.

In April 1943, the squadron became non-operational and moved to Canberra to re-equip with Bristol Beauforts and Lockheed Venturas. Initially, the Squadron's Venturas comprised a mix of the USAAC B-34 and the USN PV-1. (The Squadron relinquished its last B-34 on 5 May 1944). During November and December, a detachment of Beauforts conducted maritime patrols from Coffs Harbour, NSW. With effect from 27 December 1943, the Beauforts were handed over to 2 Squadron and 3 Squadron detached three Venturas to Camden, NSW from where they continued maritime patrols off the east coast.

On 8 June 1944, the Squadron's Venturas departed for Cooktown, Queensland. An advance party of eight aircraft departed Cooktown for Gove in the Northern Territory on 16 August 1944. From its new base at Gove, the Squadron conducted anti-submarine patrols and strikes into the Netherlands East Indies and Timor.

On 12 June 1945, the S.S William H Seward sailed from Darwin with an advance party from 13 Squadron to a destination "believed to be Morotai". The ship duly arrived in Morotai on 26 June only to be quarantined because of a case of meningitis on board. It was not until 2 July that quarantined personnel were able to disembark! The majority of personnel who were not quarantined had proceeded to Labuan by 28 June leaving only a "skeleton staff" on board ship in Morotai. On 9 July, the remaining personnel sailed for Labuan on the liberty ship S.S. John H. Rossiter which arrived on 14 July. Setting up camp and maintenance facilities was "extremely heavy work" and the Squadron was forced to beg and borrow materials and equipment from other units. The camp was constructed using timber dunnage from the S.S. John H. Rossiter. The first six Venturas arrived in Labuan from Gove on 14 August commencing operations two days later. Initially the aircraft conducted patrols but by 28 August they were relegated to dropping propaganda leaflets! One week earlier, work had commenced to strip the Venturas of armament and radar, "evidently to prepare aircraft for transport purposes". On 4 September, North West Area Headquarters ordered that the ten Venturas remaining at Gove should proceed to Darwin to have their turrets removed prior returning Gove to uplift remaining personnel to Morotai. On 24 September, eleven Venturas arrived at Labuan via Morotai.

As hostilities wound down, the Venturas were used to support Dakotas and Liberators in repatriating Australian service personnel. After the Japanese surrender, the Squadron evacuated prisoners of war to Australia and operated courier flights to Singapore, Japan and Australia. One Ventura (A59-76) was detached to the 1st Tactical Air Force in Tokyo. The Squadron disbanded at Labuan on the 11th January 1946 but reformed at Darwin in July 1989 as a non-flying reserve unit.