Enactment of Law No. 32 of 2004 on Regional Government, to provide flexibility in managing resources territoriat waters. The biggest challenge in the district of South Kalimantan is a conflict between water users. This study aimed to. determine the sfafus of government agencies and determine the government priorities in conflict management of territorial waters users. The study was conducted in South Kalimantan. The method used in this study is the Institutional Development Framework. Data retrieval techniques with purposive sampling of government institutions that play a role in conflict management. The results showed that the institutional capacity of overnment approaching stabilization stage, while the Navy and DitPolair are already at the stage of stabilization. Priorities of government agencies in managing conflict consisfs of monitoring and evaluation, communication and coordination, staff appreciation, control systems, tasks and authority. Strategies institutional security apparatus consists of participation in decisions, planning participation and conflict management training.