The conflict between Indonesia and Malaysia took place mainly on the island of Borneo. The proposal that a Malaysian Federation would be formed in September 1963 comprising Malaya, Singapore, Sarawak and North Borneo, had not been welcomed by Indonesia. By early 1963, there were growing fears that Indonesia would, following the Brunei revolt in December 1962, seek to interfere, either overtly or covertly, with the process.
In May 1964 approval was given for Australian Army personnel to be deployed to Borneo for signals intelligence (SIGINT) duties. The first Army operators were in post at Labuan by June 1964.
In January 1965 the Australian Government agreed to send 3 Royal Australian Regiment (3RAR), (replaced by 4th Battalion, Royal Australian Regiment in April 1966), two squadrons of Special Air Services (SAS), members of the Royal Australian Engineers, several artillery batteries, several Royal Australian Navy (RAN) ships to patrol nearby waters and the Royal Australian Air Force (RAAF) provided fighters.
With the prospective signing by Indonesia and Malaysia of the Bangkok Accord, plans were already in place by mid-1966 for the withdrawal of the Australian Army Sigint unit from Borneo.