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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 is called Konfrontasi in the Indonesian and Malay languages.
In 1961, the island Borneo was divided by four separate states: 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 (which was later renamed Sabah). As a part of its withdrawal from its Southeast Asian colonies, the UK moved to combine its colonies on Borneo with those on 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, the Malaysian government announced that the federation would be created, depicting the decision as an internal matter, with no need for consultation. The Indonesian government saw this as a broken promise and as evidence of British imperialism.
On January 20, 1963, Indonesian Foreign Minister Subandrio announced that Indonesia would pursue a policy of Konfrontasi with Malaysia. On April 12, Indonesian volunteers — allegedly Indonesian Army personnel — began to infiltrate Sarawak and Sabah, to engage in raids and sabotage, and spread propaganda. On July 27, Sukarno declared that he was going to "crush Malaysia". On August 16, troopers of the Brigade of Gurkhas clashed with fifty Indonesian guerillas.
While the Philippines did not engage in warfare, they did break off diplomatic relations with Malaysia.
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, 16 armed Indonesian agents were captured in Johore. Activity by regular Indonesian Army over the border also increased. The British Royal Navy deployed a number of warships, including aircraft carriers, to the area to defend Malaysia and the Royal Air Force also deployed many squadrons of aircraft. Commonwealth ground forces — 18 battalions, including elements of the Brigade of Gurkhas — and three Malaysian battalions, were also committed to the conflict. The Commonwealth troops were thinly deployed and had to rely on border posts and reconnaissance by light infantry and/or the two commando units of the Royal Marines. Their main mission was to prevent further Indonesian incursions into Malaysia.
On August 17, Indonesian paratroopers landed on the southwest coast of Johore and attempted to establish guerilla groups. On September 2, 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 Army personnel.
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, after many Malaysian requests, Australia agreed to send troops to Borneo. Australian Army contingent included the 3rd Battalion of the Royal Australian Regiment and the Australian Special Air Service Regiment. There were fourteen thousand British and Commonwealth forces in Borneo by this time. According to official policy, Commonwealth troops could not follow attackers over the Indonesian border. However, units like the British Special Air Service and the Australian Special Air Service did so in secret (see Operation Claret). (The Australian government officially admitted these incursions in 1996.)
The end of confrontation
Towards the end of 1965, General Suharto came to power in Indonesia, following 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.
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