The Indonesian Reform Period following the New Order (May 1998) brought significant challenges, particularly regarding human rights issues in East Timor. This region, which had been annexed by Indonesia since 1976, came under international scrutiny due to allegations of ongoing severe human rights violations. Domestic and global pressure urged the resolution of this legacy of violence. In a short period of time, two presidents, B.J. Habibie and Abdurrahman Wahid, took different approaches in responding to demands for transitional justice and resolving this complex issue from the past.
The Era of President B.J. Habibie: A Bold Step Towards a Referendum
President B.J. Habibie (May 1998 -- October 1999) inherited a multidimensional crisis gripping Indonesia. Amidst mounting political, economic, and security pressures, Habibie was faced with the legacy of the New Order, one of which was the status of East Timor. In a bold and unexpected move on January 27, 1999, Habibie announced a referendum proposal for East Timor, offering the choice of autonomy within the Republic of Indonesia or full independence. This decision marked a radical departure from the New Order's policy, which had always asserted East Timor as the 27th province.
The motivations behind Habibie's decision were complex. First, there was international pressure from the United Nations (UN) and Western countries following the fall of Suharto. The East Timor issue had become a diplomatic stumbling block weighing down Indonesia's foreign relations. Second, Habibie viewed East Timor as a "thorn in the flesh" that significantly drained national resources and diplomatic energy, as well as posing a considerable financial burden on a country already grappling with a severe economic crisis. Third, this decision can also be seen as part of Habibie's strategy to build his own political legitimacy and position himself as a progressive reformist leader in the eyes of both domestic and international audiences.
Although the referendum decision was welcomed by the international community as a step forward toward self-determination, its implementation on the ground sparked a wave of widespread violence. Pro-integration militias formed, trained, and supported by elements of the TNI drastically increased their activities. They intimidated, assaulted, and terrorized civilians suspected of supporting independence. Reports from various sources, including the International Crisis Group (ICG) in 2021 and UN reports, highlight this pattern of systematic violence, particularly after the announcement of the referendum results on September 4, 1999, which showed an overwhelming majority in favor of independence. These events led to widespread burning, mass killings, forced expulsions, and the destruction of infrastructure in East Timor.
Habibie's decision, while paving the way for a fundamental political settlement for Timor-Leste, paradoxically created the context for massive human rights violations. The lack of control over implementation and the failure to restrain or control pro-integration militias left a "human rights debt" that had to be settled later, even when Timor-Leste's political status had been agreed upon.
The Abdurrahman Wahid Era: Efforts Toward Transitional Justice
Replacing Habibie, President Abdurrahman Wahid (October 1999--July 2001), or Gus Dur, brought a more tangible priority to human rights enforcement and transitional justice. Gus Dur's background as a respected cleric and human rights activist gave him the moral authority and strong commitment to follow up on human rights violations in East Timor, driven by sustained international pressure.
He supported the establishment of the East Timor Human Rights Violations Investigation Commission (KPP HAM) by Komnas HAM in November 1999. The KPP HAM was tasked with gathering evidence and facts regarding alleged gross human rights violations. The KPP HAM report, published in January 2000, identified patterns of gross human rights violations and recommended individual accountability from various elements, including the military, police, and civilians associated with militias. This report became an important basis for subsequent legal measures.
Following up on these recommendations and international pressure, Gus Dur supported the establishment of the East Timor Ad Hoc Human Rights Court in 2001 through Presidential Decree No. 53 of 2001, which was later reinforced by Law No. 26 of 2000 on Human Rights Courts. This was a historic milestone for Indonesia, as it was the country's first attempt to prosecute serious human rights violations domestically. Additionally, Gus Dur took significant symbolic steps, such as visiting Dili, East Timor, and formally recognizing East Timor's independence, which contributed to conflict resolution efforts and the restoration of bilateral relations.
