Following the outbreak of the Second World War, he was posted to the Darwin Mobile Force as a platoon commander in 1940 as the threat of Japanese aggression in the Pacific grew. As a regular officer in the Permanent Military Force Hughes subsequently undertook a variety of regimental, staff and training positions in 1942, including postings to Headquarters 2nd Australian Corps, the Australian Staff College and Advanced Land Headquarters, Brisbane. In 1943 Hughes was posted to Headquarters 1st Australian Corps and was involved in the amphibious landing at Nassau Bay, as a liaison officer with the American forces during the New Guinea campaign. By 1944 he was a company commander in the 2/3rd Battalion fighting the Japanese at Wewak in New Guinea, and was later involved in the amphibious landing on Tarakan in Borneo in 1945 while attached to 26th Brigade. Hughes finished the war as a major serving with the Australian Military Mission in Tokyo, in 1945–46. Hughes was married in 1947 and he and his wife Joan later had three sons, Alan, David and Geoffrey. In 1951 he assumed command of the 2nd Battalion, Royal Australian Regiment at Puckapunyal, Victoria, which was heavily involved in training officers and soldiers as reinforcements for Australian forces fighting in Korea. In July the following year Hughes took over command of the 3rd Battalion, Royal Australian Regiment in Korea, a position he filled until March 1953. His younger brother, Jim, had previously served in the battalion as a platoon commander, and had been awarded the Military Cross for his actions during the Battle of Maryang San. He too would later also reach the rank of major general. Commanding 3 RAR during the static phase of the war he believed in active patrolling, but was doubtful of the value of operations to capture Chinese prisoners and the casualties that were incurred during these missions. For his leadership which he was later awarded the Distinguished Service Order. In 1956, Hughes was posted as a student to the Joint Services Staff College in the United Kingdom, and later instructed there. In 1964 he went to Indonesia as Military Attaché during the Indonesia–Malaysia confrontation. Returning to Australia in 1966, Hughes was promoted to brigadier, taking over command of the Queensland-based 6th Task Force. During 1967–68 Hughes commanded the 1st Australian Task Force based in Phuoc Tuy Province, South Vietnam, which was involved in counter-insurgency operations against the Viet Cong. Hughes took over command from Brigadier Stuart Graham on 20 October 1967. By the second half of 1967 the Viet Cong seemed to have melted away in Phuoc Tuy Province, abandoning many of their bunker systems and avoiding the main roads and towns, causing Graham to speculate that the Viet Cong may have fled to the border, perhaps leaving the province altogether. Meanwhile, 1 ATF was reinforced, with 3 RAR arriving in December 1967 to bring the task force up to full strength with three infantry battalions supported by armour, artillery, aviation and engineers. Throughout 1968 1 ATF spent much of its time deployed away from Phuoc Tuy Province, assisting US forces countering a number of major offensives. Hughes' period in command witnessed heavy fighting during Operation Coburg, which was mounted in response to the communist Tet Offensive, and the Battle of Coral–Balmoral. For this he was subsequently made a Commander of the Order of the British Empire. Hughes returned to Australia in October 1968. He subsequently filled the position of Director Military Operations and Plans, Army Headquarters. In 1974 he was posted as General Officer Commanding1st Division, a position he held until 1975. During his career he commanded a platoon, a company, a battalion, a brigade and a division. Finally, he was posted as Chief of the Reserve, Army Headquarters, before retiring in 1977.
Later life
In his later life Hughes was actively involved in the Returned and Services League of Australia, the United Services Institution and the Military History Society of Australia. During his retirement he was a keen gardener and tennis player and he and Joan later travelled around Australia for six months in a caravan. Hughes died in Canberra on 2 February 2003, aged eighty-two.