The paper examines the evolution of security sector governance (SSG) in Indonesia, focusing in particular on the effects of security sector reform (SSR) on the management of the secessionist conflicts in the country. It discusses the military's use of force as an instrument of conflict management in the years immediately following Indonesia's independence, arguing that while it is possible to suppress conflicts through military force, such a strategy brings about several problems. The underlying causes of the conflicts may remain unaddressed, and military impunity could increase. These could lead to rising resentment, and eventually escalation of conflicts, as occurred in Indonesia in the late 1990's. This paper argues that to resolve such conflicts, SSR is vital, and it illustrates this through the case of Aceh as an instance of successful resolution of conflict achieved against a backdrop of reform of the military sector.