The Indonesia–Malaysia confrontation () was fought from 1962 to 1966 between the British Commonwealth and Indonesia. Indonesia, under President Sukarno, sought to prevent the creation of the new Federation of Malaysia that emerged in 1963, whilst the British Commonwealth sought to safeguard the security of the new state. The war remained a limited one however, and was fought primarily on the island of Borneo, although a number of Indonesian seaborne and airborne incursions into the Malay Peninsula did occur.Dennis et al (1995), p. 171. As part of Australia's continuing military commitment to the security of Malaysia, Australian army, naval and air force units were based there with the Far East Strategic Reserve, mainly in the 28th Commonwealth Infantry Brigade Group.

The Australian Government was initially reluctant to become involved in the conflict, and Australian forces did not see combat until 1964. Australia's involvement expanded in 1965, however, following repeated requests from the British Government with an Australian infantry battalion and special forces being deployed to Borneo where they were involved in a number of actions against Indonesian Army units. Other army units deployed included artillery batteries and engineers, both of which served tours in support of the infantry in Borneo. A number of RAN warships also patrolled the waters off Borneo and Malaysia to deter Indonesian infiltration parties, and were involved in shelling Indonesian positions in Borneo and in repelling infiltrators in the Singapore Strait.Dennis et al (1995), p. 173. The RAAF played only a relatively minor role, although it would have been used far more extensively had the war escalated.A number of contingency plans existed, although none were ever fully implemented. For instance: Plan Spillikin, Plan Hemley, Plan Shalstone (renamed Mason), Plan Addington, and Plan Althorpe. These plans called for different levels of commitment depending on different contingencies, including using the majority of Australian air, land and naval forces in the Strategic Reserve, such as the Canberra bombers already based at Butterworth, as well involvement in the defence of Malaysian airspace from Indonesia attacks, air attacks on Indonesian bases by Australian aircraft flying from Australian bases and even the use of facilities in Darwin by the RAF Strategic V Bomber Force. See Dennis and Grey (1996), p. 196.

22 Australians died during the conflict, of whom 6 were killed in action or died from combat related injuries.

Background In early 1963 the Indonesian Government adopted a policy of destabilising and ultimately breaking up Malaysia, which was to become independent of the United Kingdom in September 1963. Small parties of Indonesian Army troops disguised as Malaysian insurgents were infiltrated into Malaysian territory in Borneo to spread propaganda and conduct sabotage during 1963, and several major raids were conducted against Malaysian Army and security forces bases. More attacks were conducted in 1964, with the Indonesians expanding the conflict by openly employing regular Army units and conducting raids in peninsular Malaysia. These attacks raised the risk of a general war between Malaysia and Indonesia.Dennis et al (2008), p. 152.

During the early 1960s Australian military units were based in Malaysia as part of the Far East Strategic Reserve and whilst Australian units had participated in the Malayan Emergency between 1948 and 1960, the Australian Government was reluctant to become involved in fighting with Indonesia. This was due at least in part to a fear that any such fighting would spread to the long and indefensible border between Indonesia and the Australian-administered Territory of Papua and New Guinea. Accordingly, several requests from the British government during 1963 and 1964 to deploy forces to Borneo were rejected.

Ground operations

Peninsular Malaysia 1964

Although not initially agreeing to send troops to Borneo, in April 1964 the Australian Government agreed to allow its forces to be used to protect peninsular Malaysia from attack, whilst also announcing that it would dispatch an engineer construction squadron to Borneo, while also providing two naval mine-sweepers, four helicopters and other support in addition to units already stationed in Malaysia. Meanwhile, in June the 111th Light Anti-Aircraft Battery deployed to Butterworth in northern Malaysia to defend the airfield in case the Indonesians conducted an unexpected air raid.Horner (1995), p. 462. The 3rd Battalion, Royal Australian Regiment (3 RAR), which was based at Camp Terendak in Malacca, was subsequently used to mop up two small airborne and seaborne landings near Labis and Pontian in September and October 1964. These incursions seemed to suggest a serious escalation in the conflict was imminent.

Borneo 1965–66 Following a direct request from the Malaysian Government in January 1965, Australia agreed to deploy an infantry battalion to Borneo.Grey (2008), p. 232. Units arrived in Borneo in early 1965. 1 Squadron, Special Air Service Regiment (SASR) arrived in February and was followed by 3 RAR in March. Engineer units were also deployed to Borneo where they conducted field engineering and construction tasks, whilst artillery was also deployed.Coates (2006), p. 334.Horner (1995), p. 464. The Malaysian Government later requested a second Australian battalion, however this was declined as the army lacked the resources needed for such a deployment.

During the early phases of the war, the British and Malaysian troops attempted only to control the Malaysian/Indonesian border, and to protect population centres from Indonesian attacks. However, by the time the Australian battalion had been deployed, the British had decided to take more aggressive action, crossing borders to obtain information and forcing Indonesia to remain on the defensive on their side of the border, under the codename Operation Claret. The fighting often took place in mountainous, jungle-clad terrain, and a debilitating climate. A number of features characterised military operations at this time, including the extensive use of company bases sited along the border, cross-border operations, the use of helicopters for troop movement and resupply, and the role of human and signals intelligence in helping to determine enemy movements and intentions.

3 RAR deployed to Borneo in March 1965, and served there until the end of July, conducting a number of operations on both sides of the border. During this period it was one of 12 battalions in Malaysian Borneo and operated in Sarawak as part of the West Brigade.Coates (2006), p. 335. The battalion manned defensive positions and conducted patrols to detect infiltration parties. 3 RAR also conducted 32 secret 'Claret' operations in which one or two platoon-strong parties entered Indonesian territory to ambush Indonesian forces. The battalion had four major contacts with Indonesian forces and many smaller ones—including two major ambushes on the Sungei Koemba river, another at Kindau and again at Babang between May and July—with all ending in success. These operations inflicted significant casualties on Indonesian forces and allowed 3 RAR to dominate the border area, as well as providing early warning of incursions into Sarawak and contributing to the wider success of the British-Commonwealth forces in slowly asserting control on the war.Horner (2002), p. 141. 3 RAR completed its tour in August 1965 and returned to Camp Terendak. The battalion suffered three men killed in action in two separate land mine incidents during its time in Borneo.

During its tour in Sarawak, 3 RAR had been supported by artillery from the 102nd Field Battery, Royal Australian Artillery, which also operated in support of a number of British battalions in West Brigade. The battery had deployed to Sarawak from its base at Terendak in Malaysia in late April 1965, and was attached to the British 4th Light Regiment. Operating 105 mm L5 pack howitzers, it provided indirect fire support to a number of cross-border Claret operations. In October 1965 the battery returned to Australia, and was replaced at Terendak by A Field Battery, Royal Australian Artillery, and although the latter was warned out for operations in Sarawak it was never deployed.Horner (1995), pp. 464–467.

The 4th Battalion, Royal Australian Regiment (4 RAR) arrived in Malaysia in September 1965 to replace 3 RAR, which returned to Australia in October. After a period of training the battalion deployed to Sarawak in April 1966 where it was to operate from four company bases in the Bau area. By this time the war was winding down as peace negotiations had begun between Malaysia and Indonesia.Kuring (2004), p. 305 Like 3 RAR, 4 RAR conducted cross-border operations and clashed with Indonesian forces on a number of occasions.Dennis et al (2008), p. 154. Its tour was less eventful, however, and the battalion primarily operated in Malaysian territory where it ambushed tracks leading from the border with Indonesia. Malaysia and Indonesia agreed to a peace treaty on 11 August and 4 RAR and the other Commonwealth units in Borneo ceased operations the next day. The battalion returned to Camp Terendak on 30 August having suffered five fatalities in Borneo, though only one man had been killed in action.

Australia also deployed two SASR squadrons during the conflict, marking the regiment's operational debut. 1 Squadron conducted reconnaissance patrols in Sarawak from February to July 1965, and conducted cross-border operations between May and July.Horner (2009), pp. 46–82. They suffered their first fatality on 2 June when Lance-Corporal Paul Denehey was gored by an elephant.Horner (2009), pp. 68–71. 2 Squadron arrived in Borneo in January 1966 for a four-month deployment, and despite the suspension of Claret operations it also conducted reconnaissance patrols and cross-border operations, undertaking a total of 45 patrols on both sides of the border until being withdrawn in July.Dennis and Grey (1996), p. 307. Two members of the squadron drowned while trying to cross a river during a patrol on 20–21 March.Horner (2009), pp. 89–101. SASR patrols inflicted significant casualties on the Indonesians throughout the war, even though they were often tasked with covert reconnaissance.Horner (1989).

New Guinea–Indonesia border In addition to operations in Malaysia, Australian troops patrolled the Indonesia-Papua New Guinea border during the confrontation. These operations were conducted by the Pacific Islands Regiment (PIR), which was an Australian Army formation manned by native New Guineans and led by Australian officers and warrant officers. Although there was only one shooting incident between the PIR and Indonesian troops, a number of incursions took place and these patrols–which were often conducted in rugged terrain–placed considerable demands on Australia's already limited defence resources. The PIR was also expanded from one to two battalions in 1963 in response to the increased threat posed by Indonesia, though a third battalion authorised in 1964 was not formed.Dennis et al (2008), p. 404 Other precautions included the construction and upgrading of a number of airfields in Papua New Guinea for use by the RAAF.

Naval operations

The Royal Australian Navy's (RAN's) involvement in the Confrontation also began in 1964. At this time two Australian destroyers or frigates were always in Malaysian waters as part of the FESR and other warships, including the aircraft carrier , made periodic visits. The Australian warships served as part of a fleet of up to eighty warships whose mission was to defeat attempts to infiltrate Indonesian Army units by sea, provide naval gunfire support and prevent piracy.Coates (2006), p. 336.