The Indonesia @-@ Malaysia confrontation was fought from 1962 to 1966 between the British Commonwealth and Indonesia over the creation of the Federation of Malaysia , with the Commonwealth attempting to safeguard the security of the new state . The war remained limited , and was fought primarily on the island of Borneo , although a number of Indonesian seaborne and airborne incursions onto the Malay Peninsula did occur . As part of Australia 's continuing military commitment to the security of Malaysia , army , naval and airforce units were based there as part of the Far East Strategic Reserve . Regardless the Australian government was wary of involvement in a war with Indonesia and initially limited its involvement to the defence of the Malayan peninsula only . On two occasions Australian troops from 3 RAR were used to help mop up infiltrators from seaborne and airborne incursions at Labis and Pontian , in September and October 1964 .