The border area is particularly prone to disputes and conflicts, especially those affecting national security. We address this subject specifically from the standpoint of non-military defence, with its multiple threat dimensions. We identify the border area as a site where civilmilitary relations could be investigated, particularly how civilian-dominated authorities effectively supervise and accomplish complex goals in defence as a military domain. We focus our study on the Indonesia-Malaysia border region, particularly West Kalimantan-Sarawak, taking into account both historical and contemporary developments. We conclude that a collaborative institutional role following Concordance Theory is essential in managing border areas vulnerable to multidimensional threats. Similar research that discusses the role of institutions in a comprehensive and holistic manner can be put forward for future research.