Indonesian Confrontation, 1963–66
From:
http://www.awm.gov.au/atwar/confrontation.htm
Between 1962 and 1966 Indonesia and Malaysia fought a small, undeclared war which came to involve troops from Australia and Britain. The conflict resulted from a belief by Indonesia's President Sukarno that the creation of the Federation of Malaysia, which became official in September 1963, represented an attempt by Britain to maintain colonial rule behind the cloak of independence granted to its former colonial possessions in south-east Asia.
The term "Confrontation" was coined by Indonesia's Foreign Minister, Dr Subandrio, in January 1963, and it has come to refer to Indonesia's efforts at that time to destabilise the new federation, with a view to breaking it up. The actual war began when Indonesia launched a series of cross-border raids into Malaysian territory in early 1963.
The antagonism that gave rise to Confrontation was already apparent in December 1962, when a small party of armed insurgents, with Indonesian backing, attempted to seize power in the independent enclave of Brunei, only to be defeated by British troops from Singapore. By early 1963 military activity had increased along the Indonesian side of the border in Borneo, as small parties of armed men began infiltrating Malaysian territory on propaganda and sabotage missions. These cross-border raids, carried out by Indonesian "volunteers", continued throughout 1963; by 1964 Indonesian regular army units had also become involved.

Malaya, 29 October 1964: captured infiltrators emerge from the jungle near Sungei Kesang, South of Terendak. D Coy 3 RAR troops guard them
AWM P01499.003
Australian units which fought during Confrontation did so as part of a larger British and Commonwealth force under overall British command. Australia's commitment to operations against Indonesia in Borneo and West Malaysia fell within the context of its membership in the Far East Strategic Reserve.
At first the Australian government kept its troops from becoming involved in Confrontation, not least because of fears that the conflict would spread to the long - and difficult to defend - border between Papua New Guinea and Indonesia. Requests from both the British and Malaysian governments in 1963-64 for the deployment of Australian troops in Borneo met with refusal, though the Australian government did agree that its troops could be used for the defence of the Malay peninsula against external attack. In the event, such attacks occurred twice, in September and October 1964, when Indonesia launched paratroop and amphibious raids against Labis and Pontian, on the south-western side of the peninsula. Members of the 3rd Battalion, Royal Australian Regiment (3 RAR) were used in clean-up operations against the invading troops. Although these attacks were easily repelled, they did pose a serious risk of escalating the fighting; the Australian government relented in January 1965 and agreed to the deployment of a battalion in Borneo.
The military situation in Borneo thus far had consisted of company bases located along the border between Indonesia and Malaysia to protect centres of population from enemy incursions. By 1965 the British government had given permission for more aggressive action to be taken, and the security forces now mounted cross-border operations with the purpose of obtaining intelligence and forcing the Indonesians to remain on the defensive on their own side of the border. Uncertain where the Commonwealth forces might strike next, the Indonesians increasingly devoted their resources to protecting their own positions and correspondingly less on offensive operations, although these continued on a much reduced scale.

Sarawak, British North Borneo, 1965: soldiers of 3 RAR board a Belvedere helicopter to search for Indonesian infiltrators.
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