John Martinkus – As Australia contemplates renewed military ties with Kopassus, Indonesia's special forces, the people of Papua fear an increase in military operations against their pro-independence leaders by the same organisation.

Indonesian security forces have been carrying out a program of political assassinations that began with the killing of the popular leader Theys Eluay last November and have allegedly claimed the lives of at least another two leaders from the same pro-independence body, the Papuan Presidium Council, this year. Ironically, one of the 12 Kopassus members charged with Theys' killing was trained in Australia on a young officer exchange program. A similar joint program, suspended due to the military abuses in East Timor, is being proposed again by Foreign Minister Alexander Downer to instruct officers in counter-terrorism.

The military was widely blamed for the poisoning of Yafet Yelemaken, a leader from the PNG Highlands, on June 23, while another Presidium member from Fak Fak, in the province's west, was alleged to have met a similar fate. Another leader, Benny Wenda – held in prison in the capital Jayapura – was the victim of a jail axe attack by a man he identified as being in the employ of Kopassus. An assistant who intervened was seriously injured with axe blows all over his body.

Tapol, an organisation that campaigns against human rights abuses in Indonesia, issued a report last month stating it had received leaked documents detailing a current Indonesian police operation in Papua, codenamed Adil Matoa, which aimed to build cases against Papuan organisations that supported independence in order to arrest their leaders and dissolve their organisations. The documents, signed by the head of the Papua police force, Made Mangku Pastika, list all the traditional Papuan organisations alongside the OPM (Free Papua Movement) and state they challenge the authority of the central government of Indonesia by not accepting Jakarta's autonomy plan. The leaked documents also say these organisations "make use of global issues such as human rights or the handling of the Theys case in order to achieve an independent West Papua". In other words, organisations that complain about human rights abuses are now technically illegal. Pastika has been put in charge of the investigation into the Bali bombings.

The police operation has long been feared by Papuan independence organisations monitoring the emergence of military-sponsored militia organisations and the arrival of Laskar Jihad Islamic fighters from nearby Ambon in the past two years. Many Papuan church officials and leaders have drawn links between the Indonesian military in the province and the unhindered arrival of thousands of Laskar Jihad troops. Laskar Jihad officially disbanded hours before the bomb blast in Bali and 700 members have reportedly left Ambon, where they have been embroiled in the sectarian violence on the side of the Muslims, in many cases with the assistance of the Indonesian army. Papuan church leaders have reported Laskar Jihad still present and active in Papua despite the disbandment.

Papuan leaders have also claimed that thousands of young migrants have been sent to the province this year, paid for by the Indonesian military, to act as a recruiting pool for the formation of militia and Laskar Jihad groups. Thom Beanal, leader of the Papuan Presidium Council, which proposes a non-violent path to independence and is trying to declare Papua "a zone of peace", says the military-sponsored movement of people to the province is intended to provoke violence between Christian Papuans and Muslim settlers.

But in the camps of the OPM-TPN (armed forces of the Free West Papua movement) along the Papua-PNG border, the men are training again. They have a few old weapons; most parade with sticks, spears and bows and arrows, pretending they are guns. The message from the commander, Mathias Wenda, is blunt: "We don't want autonomy and the governments of the US and Australia should convince Indonesia to get out."

In the wake of the Bali bombings and proposed increased links between the Australian military and the Indonesians, this seems unlikely. The inevitable abuses by the Indonesian military as it deals with independence movements in Papua and Aceh will attract little attention as that same military is courted by Australia and the US to take action against those responsible for the Bali attacks. But in Papua, the Indonesian military has sided with Islamic organisations to fight against Papuans who call for independence.

[John Martinkus is the author of Quarterly Essay £7, Paradise Betrayed: West Papua's Struggle for Independence, Black Inc, $11.95.]