Returning to Australia in 1954, McNamara was posted to Headquarters Training Command as pilot training officer. In 1955–56 he served as staff officer fighter operations at the Department of Air, before undertaking training at RAAF Staff College. He was Commanding Officer No. 25 Squadron at Pearce, Western Australia, in 1957–58, receiving promotion to wing commander on 1 July 1957. He took charge of No. 2 Operational Conversion Unit (No. 2 OCU) at RAAF Base Williamtown, New South Wales, in 1959. No. 2 OCU was responsible for training pilots to fly the CAC Sabre jet fighter, which was operated by Nos. 3, 75 and 77 Squadrons. His performance as commanding officer earned him the Air Force Cross in the 1961 Queen's Birthday Honours.