Indonesia's political system has undergone dramatic structural change since the 1998 downfall of the New Order regime that had ruled the country for more than three decades. A multitude of political parties has replaced the tightly controlled three-party system; free and fair elections were held that resulted in three successive coalition governments with a weakening presidency; political power was transferred from the once omnipotent centre into the regions; the previously sacrosanct constitution was extensively rewritten; civil society organizations have mushroomed; and one of the most diverse media landscapes in Asia has emerged. One area that has seen some of the most significant changes is the security sector. Indonesia's armed forces (TNI, Tentara Nasional Indonesia) had to give up their institutional engagement in politics, accept their removal from the DPR (Dewan Perwakilan Rakyat, People's Representative Council) and the MPR (Majelis Permusyawaratan Rakyat, People's Consultative Assembly), and were mandated by law to reduce their role in domestic security affairs. The police, formerly a part of the armed forces, were separated from the military and assigned the task of managing internal security.

The extent of institutional reform affecting Indonesia's security sector has led some observers to the conclusion that “the civil-military balance has tilted against the military, and state-soldier relations are in the midst of substantial change” (Alagappa 2001a, p. 16). In this view, the reform movement has weakened the armed forces substantially, rushing in a new class of civilian politicians that has taken charge of the country.