Indonesia's opposition to the 1963 establishment of the Federation of Malaysia presented the only known external threat to Singapore since Japanese occupation. The opposition of Indonesian President Sukarno to the incorporation of Sabah and Sarawak on the island of Borneo into the Federation of Malaysia set up the early stages of a low-intensity conflict called Confrontation, which lasted three years and contributed to Sukarno's political demise. In August 1963, Indonesia deployed several thousand army units to the Indonesian-Malaysian border on Borneo. Throughout the latter part of 1963 and all of 1964 the Indonesian army dispatched units, usually comprising no more than 100 troops, to conduct acts of sabotage and to incite disaffected groups to participate in an insurrection that Djakarta hoped would lead to the dissolution of the Federation. In June and July 1964, Indonesian army units infiltrated Singapore with instructions to destroy transportation and other links between the island and the state of Johor on the Malay Peninsula. Indonesia's Kalimantan Army Command also may have been involved in the September 1964 communal riots in Singapore. These riots occurred at the same time Indonesian army units were deployed to areas in Johor in an attempt to locate and encourage inactive communists in the Chinese communities to reestablish guerrilla bases destroyed by British and Malaysian military units during the Emergency. After September 1964, Indonesia discontinued military operations targeting Singapore. In March 1965, however, a Singapore infantry battalion deployed on the southern coast of Johor was involved in fighting against a small Indonesian force that was conducting guerrilla operations in the vicinity of Kota Tinggi. Indonesia supported Singapore's separation from Malaysia in 1965 and used diplomatic and economic incentives in an unsuccessful effort to encourage the Lee administration to sever its defense ties with Malaysia and Britain. In March 1966, General Soeharto, who until October 1965 was deputy chief of the Kalimantan Army Command, supplanted President Sukarno as Indonesia's de facto political leader. Soeharto quickly moved to end the Confrontation and to reestablish normal relations with Malaysia and Singapore.

Data as of December 1989