Borneo/Malaysia 1962-1966
The Indonesia-Malaysia confrontation was an intermittent war over the future of the island of Borneo between British-backed Malaysia
and Indonesia from 1962 to 1966.

In 1961, the island of Borneo was divided into 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 centres 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” or in Indonesian Malay “Ganyang Malaysia”. On August 16, troopers of the Brigade of
Gurkhas clashed with fifty Indonesian guerrilas.

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.

In 1964, Indonesian troops began to raid areas in the Malaysian peninsula.

In August, sixteen armed Indonesian agents were captured in Johore. Activity by the 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, fifty-two 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 non-permanent 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. The 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 (‘Operation Claret’, which was officially admitted by the Australian government in 1996.)

On March 10 1965, Indonesian saboteurs carried out the MacDonald House bombing in Singapore killing three people and injured thirty-three.

In mid-1965, the Indonesian government began to openly use Indonesian army forces. On June 28, they crossed the border into Eastern Sebatik Island near Tawau, Sabah, and clashed with defenders.

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.