Australia's involvement in the Indonesian Confrontation followed a similar pattern to involvement in the Malayan Emergency – initial government hesitation gave way to escalation until the commitment peaked during the conflict's later stages.
When the New Federation of Malaysia came into being in September 1963, both Malaysia and Britain asked whether Australian troops could be sent to Borneo to help repel Indonesian-backed incursions. The Australian Government wavered. Although Prime Minister Menzies had spoken publically of his desire to help Malaysia, other members of Cabinet felt that Britain – not Australia – should be doing more. The United States also warned against open conflict with Indonesia. The Australian Minister for External Affairs, Garfield Barwick, therefore announced 'a carefully graduated response' to the British and Malaysian requests.
After further requests and Commonwealth talks held in Bangkok in March 1964, Australia agreed to supply Malaysia with stores and military equipment, and to train Malaysian soldiers in both Australia and Malaysia. In April 1964 a squadron of Australian engineers was sent to Borneo and two Australian Navy minesweepers were made available to patrol the area. Nevertheless the official position remained that Australian ground troops already in Malaysia as part of the 28th Commonwealth Brigade were only to be used to defend the mainland against external attack. In September 1964 the Indonesians did in fact begin paratroop and amphibious raids on mainland Malaya. Members of the 3rd Battalion, the Royal Australian Regiment (3 RAR) assisted in operations against the invaders, and in December 1964 the minesweeper HMAS Teal exchanged fire with an Indonesian vessel off Singapore.
In January 1965 the Australian Government responded to this expansion of the conflict by agreeing to the deployment of 3 RAR to Borneo. A second Australian infantry battalion (4 RAR), Special Air Service squadrons, and Australian artillery and engineer units also served in Borneo before the end of the Confrontation in August 1966. In addition, Sabre jet fighters of No.78 Wing RAAF began deploying from Butterworth airbase to Labuan in Borneo in September 1965, and 12 Royal Australian Navy vessels attached to the British Commonwealth Far East Strategic Reserve patrolled Malaysian waters at various stages during the conflict. Seven Australians died on active service in the Indonesian Confrontation.