Human Rights Watch has urged Indonesia's military commander to institute changes in, among other things, the applicability of civilian criminal justice to military personnel:
Allow Civilian Prosecutions of TNI Human Rights Abuses
Indonesia’s military justice system continues to lack the transparency, independence, and impartiality required to properly and fairly investigate and prosecute serious human rights violations.
Under Indonesian law, military personnel cannot be tried in civilian courts, with only a few rarely invoked exceptions. The 1997 Law on Military Courts provides that such courts have jurisdiction to prosecute all crimes committed by soldiers. Additionally, the 1997 Law on Military Courts states that military courts can only apply one of two laws: the Military Penal Code and the general Criminal Code. This means that while civilians are subject to a criminal liability under a host of criminal laws outside the Criminal Code, soldiers are not. While the 2000 Law on Human Rights Courts authorizes human rights courts to assert jurisdiction over cases involving allegations that military personnel committed serious human rights violations, at present the law applies only to allegations of genocide and crimes against humanity, and not to the broad spectrum of conduct that constitutes human rights abuses.
During the United Nations Universal Periodic Review of Indonesia’s human rights record in 2007 and again in 2012, the Indonesian government committed to reforming the military tribunal system. The promised reforms included adding torture and other acts of violence to the military criminal code of prosecutable offenses and ensuring the definition of those offenses are consistent. However, to date the government has not added those offenses to the military criminal code.
Although the 2004 Armed Forces Law placed the military courts under the supervision of Indonesia's Supreme Court, in practice the military continues to control the composition, organization, procedure, and administration of the military courts. Military judges can be dismissed by an Honorary Board of Judges whose members are designated by the military commander.
The poor record of Kopassus [Special Forces Command] for human rights violations and its failure to hold the abusers accountable spans its operations across Indonesia, beginning in the 1960s in Java and extending to Kalimantan, East Timor, Aceh, and Papua in the decades since. The well-documented East Timor abuses prompted the United States to impose a ban on military contact with the elite force in 1999. In 2010, the US lifted the ban. Human Rights Watch and domestic human rights organizations criticized the lifting of the ban on the basis that the Indonesian military, and Kopassus in particular, had failed to demonstrate a genuine commitment to accountability for serious human rights abuses.
Empowering civilian courts to prosecute military personnel implicated in human rights abuses against civilians is a crucial step for ending Indonesia’s long and pervasive culture of impunity for military abuses.The full text of HRW's letter can be found here.