Below is an article published by The Telegraph UK

 Johan Teterisa was sentenced to life in prison for treason after dancers performing for President Susilo Bambang Yudhoyono and dozens of dignitaries in 2007 unfurled the independence flag for Republic of South Maluku flag. The development created uproar and prompt[ed] Yudhoyono to take over the microphone, ordering their arrest. Other colleagues who had displayed the flag received sentences of seven to 20 years.

The country's military took a step back from politics a decade ago but human rights groups point out that massacres committed by troops in East Timor, Papua, Aceh, Maluku, Kalimantan have not been examined in the courts.

The murder of Munir Thalib, a well regarded human rights defender who was fatally poisoned on a Garuda Indonesia flight in 2005 remains unresolved. Evidence has pointed to the involvement of high-ranking intelligence officers in the attack.

A range of journalists and activists who have taken on entrenched political or economic interests have been subjected to criminal defamation charges.

Everyday acts – such as complaining about treatment received at a hospital or asking a local official about a land assessment – can result in a defamation prosecution and a prison sentence.

Activists outside the country have pursued abuses in Western courts. ExxonMobil faced claims it aided and abetted murder, torture and sexual assault by its security forces in Indonesia's Aceh province.

Indonesian villagers claimed ExxonMobil was responsible for the abuses because they were committed by an Indonesian military unit dedicated only to Exxon's Aceh facility and under the company's direction and control.

Exxon provided material support to the unit by hiring mercenaries for training, advice and intelligence, the villagers alleged. The human rights abuses began in the early 1990s, according to one of the complaint.

Even when complaints are prosecuted, the actions have been criticised as inadequate.

A 10-minute, mobile-phone video, published last October, showed soldiers kicking Tunaliwor Kiwo, a Papuan farmer, in the face and chest, burning his face with a cigarette, and applying burning wood to his penis.

The soldiers placed a knife to the neck of the other man, Telangga Gire, while threatening to kill him. According to Kiwo the torture lasted for three days.

The soldiers beat him with their hands and sticks, crushed his toes with pliers, suffocated him with plastic bags, burned his genitals and other body parts, cut his face and head and smeared the wounds with chillies.

But military prosecutors did not bring torture charges and only three of the soldiers were charged with minor offences.