RAF Avro Vulcan bomber lands at RAF Butterworth, Malaysia, c 1965. The presence of these strategic bombers was a considerable deterrent to the Indonesians during the Confrontation period
The conflict lasted nearly four years; however, following General Suharto's successful coup against Sukarno, Indonesian interest in pursuing the war with Malaysia declined, and combat eased. Peace negotiations were initiated during May 1966 before a final peace agreement was ratified on 11 August 1966.
British Commonwealth forces peaked at 17,000 deployed in Borneo, with another 10,000 more available in Malaya and Singapore.[
Total British Commonwealth military casualties were 114 killed and 181 wounded. Australian casualties of 16 killed and 9 wounded Indonesian casualties were estimated at 590 killed, 222 wounded and 771 captured
Following Indonesia's diplomatic victory in the West New Guinea dispute, Sukarno may have been emboldened to extend Indonesia's dominance over its weaker neighbours. Sukarno argued that Malaysia was a British puppet state, a neo-colonial experiment, and that any expansion of Malaysia would increase British control over the region, with implications for Indonesia's national security.
Co-ordinated to coincide with Sukarno announcing a 'Year of Dangerous Living' during Indonesian Independence Day celebrations, Indonesian forces began a campaign of airborne and seaborne infiltrations of the Malaysian Peninsula on 17 August 1964. On 17 August 1964 a seaborne force of about 100, composed of airforce Pasukan Gerat Tjepat (PGT — Quick Reaction Force) paratroopers, KKO and about a dozen Malaysian communists, crossed the Malacca Straits by boat, landing at Pontian in three parties in the night. Instead of being greeted as liberators, however, they were contained by various Commonwealth forces and all but four of the infiltrators were captured within a few days. On 2 September, three Lockheed C-130 Hercules aircraft set off from Jakarta for Peninsula Malaysia, flying low to avoid detection by radar. The following night, two of the C-130 managed to reach their objective with their onboard PGT paratroopers, who jumped off and landed around Labis in Johore (about 100 miles north of Singapore). The remaining C-130 crashed into the Malacca Straits while trying to evade interception by an RAF Javelin FAW 9 launched from RAF Tengah. Due to a lightning storm, the drop of 96 paratroopers was widely dispersed. This resulted in them landing close to 1/10 Gurkhas, who were joined by 1st Battalion, Royal New Zealand Infantry Regiment (1 RNZIR) stationed near Malacca with 28 (Commonwealth) Brigade. Operations were commanded by 4 Malaysian Brigade, but it took a month for the security force to capture or kill 90 of the 96 parachutists, for the loss of two men killed during the action.
Indonesia's expansion of the conflict to the Malaysian Peninsula sparked the Sunda Straits Crisis, involving the anticipated transit of the Sunda Strait by the British aircraft carrier HMS Victorious and two destroyer escorts. Commonwealth forces were readied for airstrikes against Indonesian infiltration staging areas in Sumatra if further Indonesian infiltrations of the Malaysian Peninsula were attempted. A tense three week standoff occurred before the crisis was peacefully resolved.
By the concluding months of 1964 the conflict once again appeared to have reached stalemate, with Commonwealth forces having placed in check for the moment Indonesia's campaign of infiltrations into Borneo, and more recently, the Malaysian Peninsula. However, the fragile equilibrium looked likely to change once again in December 1964 when Commonwealth intelligence began reporting a build-up of Indonesian infiltration forces in Kalimantan opposite Kuching which suggested the possibility of an escalation in hostilities. Two additional British battalions were subsequently deployed to Borneo. Meanwhile, due to the landings in Malaysia and Indonesia's continued troop build-up, Australia and New Zealand also agreed to begin deploying combat forces to Borneo in early 1965.
On 28 May 1966, at a conference in Bangkok, the Malaysian and Indonesian governments declared the conflict was over. However, it was unclear if Suharto was in full control of Indonesia (rather than Sukarno), and vigilance in Borneo could not be relaxed. With Suharto's co-operation a peace treaty was signed on 11 August and ratified two days later.
During Suharto's rise to power operations continued and, in March 1966, a Gurkha battalion was involved in some of the fiercest fighting of the campaign during two raids into Kalimantan.
In addition to the ground and air force units, between 1963 and 1966 there were up to 80 ships from the Royal Navy, Royal Australian Navy, Royal Malay Navy and Royal New Zealand Navy