The Agreement to normalise relation between Malaysia and Republic ofIndonesia that resides with the National Archives of Malaysia was strong evidence that demonstrated that conflicts or tensions which existed between two neighbouring countries can be resolved at the negotiation table.

In 1963, a dark moment of history was recorded between Malaysia and Indonesia, two neighbouring nations that were regarded as twin brothers. It sparked off through a misunderstanding that subsequently aroused suspicion among the Indonesians that led to the break off in diplomatic relations between the two nations. The establishment of Malaysia that brought Singapore, Sabah and Sarawak into Malaysia, was disliked by Indonesia and the Philippines. Indonesia considered the idea of Malaysia as a new element of colonialism in this region. On the other hand, the opposition from the Philippines that was rife was based on the excuse that Sabah was theirs..

On 18 September 1963, the Malaysian Cabinet in an emergency meeting decided to break off diplomatic relations with Indonesia and the Philippines. The Ambassador of Malaysia in Jakarta, Dato' Haji Kamaruddin as well as the Malaysian embassy officials and the Ambassador of Malaysia in Manila, Encik Zaiton Ibrahim were summoned back. The Malaysian Consulate in Medan was also shut down. In Tunku's statement, this action had to be taken because Indonesia had broken off diplomatic relations with Malaysia without any clear reasons. For Malaysia, this event was a bitter test that must be faced and dealt with by all Malaysians.

Throughout the confrontation, attacks upon attacks were launched by the Indonesian guerrillas at the borders of North Borneo and Sarawak, including trespassing and the landing of Indonesian paratroopers at several places in Johor. Malaysia however did not reciprocate through violence but in turn adopted a defensive attitude.

Through the results that culminated from the mutual consultation and wisdom of leaders from both countries, the conflicts were finally contained. Several series of secret discussions were held by leaders of both countries. The first confidential discussion was held in Bangkok on 23 to 24 April 1966 between Ghazali Shafie (Malaysia) and Major-General Ali Moetopo (Indonesia). This was ensued by a second discussion between Ghazali Shafie and Adam Malik on 30 April 1966, which was also held in Bangkok. To reaffirm the stand of Jakarta for reconciliation, a goodwill mission from Jakarta that consisted of 20 military officers had arrived in Kuala Lumpur on 27 May 1966.