Ever since the days of Indonesian Konfrontasi in the 1960s, the bilateral relation between Malaysia and Indonesia have always been quite cordial, despite the occasional verbal skirmishes that is only to be expected between neighbours.

The biggest obstacle towards better bilateral relations has to be the conflicting territorial claims between the two countries. Since 1980, Indonesia has submitted 36 diplomatic protest notes to Malaysia over the issue since 1980.

In March 2005, Indonesia accused the Malaysian navy vessel, KD Renchong, of ramming its military ship, KRI Tedung Naga. The incident caused minor damage to both vessels. That incident too caused a great deal of negative excitement in the Indonesia media.