General Wiranto, along with one civilian and six senior military officials, has been charged with crimes against humanity, including murder, deportation and persecution of people who supported the East Timor independence movement.
After winning independence in 1999, people in the region renamed their country Timor-Leste.
However, the British Broadcasting Corp reported that Indonesian officials said they would ignore the indictment and refuse to hand over Wiranto.
Indonesia, which has established a human rights court to look into allegations involving Timor-Leste, and has consistently refused to have its citizens, 170 of whom have been indicted for alleged atrocities related to the East Timor vote, tried in Timor-Leste.
The U.N. serious crimes unit for Timor-Leste issued a statement alleging that militia groups had acted with Indonesian armed forces. As a result, Wiranto, military officials Suhartono Suratman and Anwar Makarim and former Gov. Abilio Soares were among those listed in the latest indictment.
Soares has been convicted in the Indonesia human rights court, but has appealed the finding.