He was promoted to temporary wing commander in April. The following month, No. 13 Squadron conducted familiarisation flights over the Dutch East Indies. Balmer handed over command of the unit in August, and transferred to a liaison post at Headquarters RAAF Station Darwin. In January 1942, Balmer briefly took charge of No. 7 Squadron, flying Hudsons on maritime patrol and convoy escort duties from RAAF Station Laverton, Victoria. Two months later he assumed command of the first RAAF unit to operate Australian-built Bristol Beauforts, No. 100 Squadron. It was formed at Richmond using the number of a Royal Air Force (RAF) squadron that had been decimated in the Malayan Campaign. In tribute to its original incarnation, Balmer adopted the RAF unit's crest, which featured a skull-and-crossbones emblem and the motto Sarang Tebuan Jangan Dijolok (Malay for "Do not stir up a hornet's nest"). No. 100 Squadron transferred to Mareeba in Far North Queensland on 22 May, after Balmer decided that a proposed base at Cairns was unsuitable owing to periodic flooding. While his crews at Mareeba gained experience on maritime patrols, he travelled to Port Moresby, New Guinea, on 26 May to test the Beaufort in operational conditions; as he came in to land he was fired upon by US anti-aircraft batteries, whose gunners had "never seen a Goddamn aircraft like that before", but escaped damage. Balmer was appointed an Officer of the Order of the British Empire in the King's Birthday Honours on 11 June 1942. On 25 June he took five of No. 100 Squadron's Beauforts to Port Moresby, joining two other Beauforts that were already stationed there. That night he led five aircraft from his squadron on their first bombing mission, against a Japanese ship reported in the Huon Gulf near Lae. Despite finding his bomb release gear faulty, necessitating three low-level attack runs in the face of increasingly heavy anti-aircraft fire, Balmer managed to score two hits, and his companions also successfully bombed the vessel. The ship appeared to be on fire and sinking, and the squadron received credit for its destruction at the time, but later investigation could not confirm its loss. The unit withdrew to Laverton for training and patrol work during July and August, before moving to Milne Bay to again take part in the New Guinea campaign. On 7 September 1942, Balmer commanded a combined force of P-40 Kittyhawks from Nos. 75