The Indonesia-Malaysia confrontation was an intermittent war over the future of the island of Borneo, between British-backed Malaysia and Indonesia in 1962-1966. It was called Konfrontasi in Indonesian and Malay language.
In 1961, Borneo was divided by four separate administrations. Kalimantan, an Indonesian province, was located in the south of the island. In the north were the kingdom of Brunei and two British colonies — Sarawak and British North Borneo, later renamed Sabah. As a part of its withdrawal from its Southeast Asian colonies, the UK moved to combine its colonies on Borneo with peninsular Malaya to form Malaysia.
This move was opposed by the government of Indonesia; President Sukarno argued that Malaysia was a puppet of the British, and that the consolidation of Malaysia would increase British control over the region, threatening Indonesia's independence. Similarly, the Philippines made a claim for Sabah, arguing that it had historic links with the Philippines through the Sulu archipelago.
In Brunei, the Indonesian-backed North Kalimantan National Army (TKNU) revolted on December 8, 1962. They tried to capture the Sultan of Brunei, seize the oil fields and take European hostages. The Sultan escaped and asked for British help. He received British and Gurkha troops from Singapore. On December 16, British Far Eastern Command claimed that all major rebel centers had been occupied, and on April 17, 1963, the rebel commander was captured and the rebellion ended.
The Philippines and Indonesia formally agreed to accept the formation of Malaysia if a majority in the disputed region voted for it in a referendum organized by the United Nations. However, on September 16, before the results of the vote were reported, Malaysia announced that the federation would be created. The Malaysians saw the creation of this federation as an internal matter, with no room for external interference, but the Indonesian leadership understood it as a broken promise and as evidence of British imperialism.
On January 20, 1963, Indonesian Foreign Minister Subandrio announced Indonesia's hostile stand against Malaysia. On April 12, Indonesian volunteers (most likely irregular army troops) begun to infiltrate Sarawak and Sabah to spread propaganda and engage in raids and sabotage. On July 27, Sukarno declared that he was going to "crush Malaysia". On August 16, troopers of the Gurkha Brigade clashed with fifty Indonesian guerillas.
While the Philippines did not engage in warfare, they did break off diplomatic relations with Malaysia.
The Federation of Malaysia was formally formed on September 16, 1963. Brunei decided against joining, and Singapore separated later.
Tensions rose on both sides of the Straits of Malacca. Two days later rioters burned the British embassy in Jakarta. Several hundred rioters sacked the Singapore embassy in Jakarta and the homes of Singaporean diplomats. In Malaysia, Indonesian agents were captured and crowds attacked the Indonesian embassy in Kuala Lumpur.
Along the remote jungle border in Borneo, there was an ongoing border war; Indonesian troops and irregulars tried to occupy Sarawak and Sabah, with little success.
In 1964 Indonesian troops began to raid areas in the Malaysian peninsula. In August, sixteen armed Indonesian agents were captured in Johore. Activity of the regular Indonesian Army over the border also increased. The British Royal Navy deployed their forces to defend Malaysia. British Commonwealth forces were formed of eighteen British battalions, including elements of the Gurkha Brigade and three Malaysian battalions. British-Malaysian troops were thinly deployed and had to rely on border posts and the reconnaissance of commando units. Their main mission was to prevent further Indonesian incursions into Malaysia.
On August 17 Indonesian paratroopers landed on the coast in the southwest of Johore and attempted to establish guerilla groups. On September 2 1964 more paratroopers landed in Labis, Johore. On October 29, 52 soldiers landed in Pontian on the Johore-Malacca border and were captured by New Zealand troops.
When the United Nations accepted Malaysia as a nonpermanent member, Sukarno withdrew Indonesia from the UN and attempted to form the Conference of New Emerging Forces (Conefo) as an alternative.
In January 1965, Australia agreed to send troops to Borneo after many Malaysian requests. Australian troops included 3 Royal Australian Regiment and the Australian Special Air Service Regiment. There were fourteen thousand British and Commonwealth forces in Borneo at this time. At least officially, British and Australian troops could not follow attackers over the Indonesian border. However, units like the Special Air Service, both the British and Australian versions, did so clandestinely (see Operation Claret). Australia admitted to these incursions in 1996.
In mid-1965, the Indonesians began to use Indonesian army regular forces. On June 28, they crossed the border into eastern Sebatik Island near Tawau, Sabah and clashed with defenders.
The end of confrontation
Towards the end of 1965, General Suharto came to power in Indonesia in the aftermath of a coup d'état. Due to this domestic conflict, Indonesian interest in pursuing the war with Malaysia declined, and combat eased.
On May 28 1966 at a conference in Bangkok, the Malaysian and Indonesian governments declared the conflict over. Violence ended in June, and a peace treaty was signed on August 11 and ratified two days later.
See: British military history, History of Indonesia, History of Malaysia