Indonesia embarks on transitioning period in 1998 after 32 years under authoritarian regime led by General Suharto. Since then the country has seen rapid changes particularly in relation to the Indonesian military (TNI). The military no longer plays role in day-to-day politics and has been returned to the barrack. New laws were enacted aiming at reforming the military and increase their professionality. Despite these positive notes, however, the military has been involved in several human rights abuses after the reformation in 1998 particularly in the region of Papua. Questions then arise as to whether democratic transition does in fact influence the military’s behavior. The answer may not as simple as it may seem; as apparent in this thesis the transitioning period in Indonesia laid rather unstable foundation for further reform efforts. Focusing on the relation between transitioning democracy and the military’s behavior this thesis aims to analyze causes and justifications which led to abuse of power by members of the military. Based on interviews to main stakeholders and other supporting data it is apparent that reform process in Indonesia has been limited at best. Serious lack of political will from the government has been one of the factors which impedes the reform effort. Moreover, the government has yet to touch upon the core problem of military off-budget funding, military territorial command and military intervention in politics.