Since independence , the country has struggled to maintain unity against local insurgencies and separatist movements . Some , notably in Aceh and Papua , have led to an armed conflict , and subsequent allegations of human rights abuses and brutality from all sides . The former was resolved peacefully in 2005 , while the latter continues , amid a significant , albeit imperfect , implementation of regional autonomy laws , and a reported decline in the levels of violence and human rights abuses since 2004 . Other engagements of the army include the campaign against the Netherlands New Guinea to incorporate the territory into Indonesia , the '' Konfrontasi '' to oppose the creation of Malaysia , the mass killings of PKI , and the invasion of East Timor , which remains Indonesia 's most massive military operation
mass killings
Indonesian mass killings of 1965–66
Indonesia