Coincident with the raising of 8MWS, 9MWS was formed at Royal Park, Victoria on 4 January 1943 and moved to Ryder Oval, Brunswick, on 26 February. Training of the unit followed an unusual course. On 17 April, the unit commenced preparation for a move the Royal Army Engineer Training Centre at Kapooka, Wagga Wagga, and New South Wales. The training, which commenced on 17 April, was wide-ranging in scope, covering field machines, water supply, explosives and demolitions, field defenses and automatic weapons. 9MWS returned to Caulfield on 10 July to load equipment stored at the racecourse, and the first body of men departed on the Terowie/Alice Springs rail link to the north a week later.
When 9WMU arrived in the Darwin area it was deficient in essential machinery and men and it was decided at a conference held at Headquarters 61 Works Wing on 6 August that selected personnel would be loaned, pending the arrival of earth moving equipment, to other works units for three weeks. It was not until early September that the unit's heavy equipment arrived and was put to good use. Work was commenced on a new flying boat base at Darwin and a detachment commenced work on the reconstruction of the runway at Coomalie Creek on 21 October. Despite an air raid on 10 November, in which five bombs dropped a mile from the 9WMU detachment campsite, the detachment worked a three-shift operation to enable 31 Squadron to return from Darwin to its home on 14 November. Although the detachment relocated its camp to Batchelor Road on 23 November, it completed the construction of taxiways at Coomalie Creek on 1 January 1944.
Even though the unit was under strength by 100 personnel at the end of November 1943, 9WMU assumed the responsibility for 3MWS activity at Batchelor and the adjacent airfield at Gould. At Gould, the unit worked a seven-hour, three shift, six day a week program, and also constructed revetments and fighter inserts at Sattler, Hughes and Livingstone as well as a taxiway at Strauss. In addition it undertook maintenance work at the Darwin civilian and RAAF airfields. There was one fatality during this period. Leading Aircraftman S.J. Hall was killed in a freak accident when he was hit by a flying rock during a blasting operation at one of the quarry faces. He died on arrival at 109ACH and was buried on 12 May 1944.
The most interesting project undertaken by 9WMU was the construction of fighter strips on Melville Island. On 27 January 1944 Wing Commander Rooney, Wing Commander Maunder, Squadron Leader Harrison, Flight Lieutenant Garden, and Flying Officer Clark flew by Catalina to reconnoiter airfield sites on the island. Before the group returned to Darwin on the following day, arrangements were made with Lieutenant Gribble at the Snake Bay naval watch station to enable the employment of some 40 Aboriginal labourers. Flight Lieutenant A.B. Cochran, the commander of 12 Survey and Design Unit who surveyed, and reported on the site, during April and May, followed up this action. Although it would not have been common knowledge at the time, the construction of the airstrips on Melville Island was in preparation for an ambitious operation being planned by RAAF Command. On 3rd March 1944 Headquarters North Western Area was directed to create a task force to support amphibious operations by Allied forces against Tanimbar and Kai islands. The dual airfield at Melville Island was to be 1,829 metres long and capable of operating a RAAF Fighter Wing Headquarters, three RAAF Fighter Squadrons, one US Fighter Group Headquarters, three US Fighter Squadrons and one Operational Base Unit, with a total of 2,290 personnel. This facility would enable long-range fighters and attack aircraft to support the assault, but priorities imposed by General Headquarters for Papua New Guinea operations meant that the project did not proceed beyond the planning stage.
Three vessels departed with the advance party and equipment from Darwin on 4 July 1944. The Southern Cross transported 25 tons of equipment and towed two barges to Snake Bay. The Army vessel King Bay was loaded with 50 tons of equipment and 20 personnel and also towed a barge, while the Amaryllis transported two men and ten tons of equipment. The landing was made across Banjo Beach and once the Southern Cross was unloaded on 6 July immediate action was taken to build the access road to the airfield site.
Due to the secrecy surrounding the project wireless silence was enforced. Commencing on 11th July, Six Communications Unit established a Walrus courier service between Batchelor and Snake Bay every second day. 24 The James Cook, Toorbul, and Amaryllis also retained links with the island. On 15 July 123 members of 9MWS and the Army 19th Works Employment Company and the 2/3rd Docks Operating Company travelled to Melville Island on the James Cook.
At the mid afternoon point of the 7th July, work on the airstrip, which involved 40 `willing, intelligent and energetic’ Aborigines, commenced. By 14th July the steel mat had been laid and was ready for service. However the construction crew had a problem grubbing out tree roots. Approximately 4,000 6,000 stumps had to be individually shattered with explosives and then removed with a power rooter and 90-horsepower tractor. The unit history record of 30 August 1944 states that `all works [had been] completed and [the airfield is] fit for operational use'. The airstrip was put to good use at midnight 31st August. The legendary 'Doc' Fenton (one of the original flying doctors and a well known Top End `character') from Six Communications Unit landed a De Havilland Dragon aircraft to evacuate a seaman from HMAS Fremantle who had been injured in a shooting accident. Trucks headlights were arranged to show a herringbone pattern of light into the wind direction.
The squadron had commenced its withdrawal on 22nd August, when work on loading the Matthew Flinders commenced. The ship departed next day, with an LCM loaded with a D 8 tractor in tow, bound for Darwin. The construction of the airfield at `Austin', as it was named, was a matter of pride to the commander, Squadron Leader Harrison. On 26th August he wrote to Wing Commander Rooney at 61 Works Wing that `the job at Melville was completed several days ago and the plant and personnel returned here better tell them at 62 [Works Wing] that 140 men from this wing built two strips in 21 days plus hardstands and incidental works'.
The squadron commenced packing for movement south on 22nd September 1944 and the first convoy departed three days later. All the squadron's heavy equipment departed from Darwin for Sydney aboard the Montoro on 5th November and the final members of the Squadron, Sergeant Quinn and five airmen, departed from Darwin four days later.