After completion and successfully performing the service with the United Nations (UN) in Congo, the Army once again come forward against the threat to the country when Indonesia, under the leadership of President Sukarno launched a confrontation against Malaysia in 1963. Confrontation is a protest against the formation of Malaysia on 16 Sep 1963 which incorporated Sabah and Sarawak with the states in Peninsular Malaysia. The standoff continued for three years, and many incidents and battles occurred between the Malaysian Army and the forces of Sukarno regime. In these battles, the soldiers have shown the spirit of heroism and sacrifices to defend national sovereignty.
One bitter event that could not be forgotten in the history of the Army is the Kalabakan incident that occurred on 29 Dec 1963. In this episode, one of the Army’s Temporary Post in Kalabakan, Tawau with the strength of a platoon under the command of Maj Zainal Abidin bin Haji Yaacob from C Company, Third Battalion Royal Malay Regiment were attacked while they were performing the Maghrib prayers. Although unprepared, the members of the platoon fought the enemy and able to force them to retreat. The attack killed seven soldiers, including Major Zainal Abidin and injured 16 others.
In Peninsular Malaysia, a lot of events happened in Batu Pahat, Pontian, Kota Tinggi and Labis in Johor. In this area, the enemy forces were infiltrating through the coastal line. They also enter through the air with parachutes in Labis on 1 September 1964. All these intrusions were denied by the Malaysian Army within few days because the enemy did not get the support or assistance from the local. Aware of this fact and due to the political pressure, President Sukarno end the confrontation towards Malaysia in 1965.