Promoted to group captain, Murdoch was appointed senior air staff officer (SASO) at Eastern Area Command, Sydney, in July 1943. In January 1944, he became SASO at North-Western Area Command, which controlled thirteen Australian, British, Dutch, and American squadrons from its headquarters in Darwin, Northern Territory. Murdoch planned many of the command's bombing and mining operations in the South West Pacific Theatre, and was mentioned in despatches for his "distinguished service" in the role. He was posted as SASO to the Australian First Tactical Air Force (No. 1 TAF) in April 1945, replacing Group Captain William Gibson after the latter's dismissal in the wake of the "Morotai Mutiny", when the threatened resignations of eight of the RAAF's leading fighter aces caused a crisis in the formation's leadership. Delegated operational responsibility by No. 1 TAF's new commander, Air Commodore Frederick Scherger, Murdoch received much of the credit for the planning of the RAAF's role in Operation Oboe Six, the invasion of Labuan. He accompanied Scherger ashore on the afternoon of the landings on 10 June 1945. Murdoch was also praised for his staff work during Operation Oboe Two, the Battle of Balikpapan, in July.