It comes as the Indonesian military is believed to be stepping up its activities in Papua and there are reports of Indonesian backed militias increasing their presence there too. Human rights groups are calling for international intervention.
HOLLAND: In an open letter to the Indonesian president more than 30 humanitarian groups jointly called for Susilo Bambang Yudhoyono to urgently review his country's military presence in Papua.
LETTER; Dear President Yudhoyono, We are writing to express our grave concern about the tenure of Col. Burhanuddin Siagian as commander of the Jayapura sub-regional military command in Papua. Col. Siagian has been indicted twice for crimes against humanity in East Timor. Indonesia has not complied with its obligations under international law and Indonesian domestic law to prosecute Col. Siagian for his alleged crimes, and it has furthermore failed to extradite him to East Timor for trial. Instead he has been promoted and appointed to command a large military unit within a highly sensitive area.
HOLLAND: According to indictments issued by the Special Panel for Serious Crimes of Dili District Court, Col. Siagian made public speeches threatening to kill East Timor's pro-independence supports.
It's believed those statements, made in 1999, directly led to the deaths of a number of Timorese civilians. Siagian has since been charged with crimes against humanity.
These include: torture; murder; persecution; and the forcible transfer of a civilian population.
According to a recently released report in the Cenderawasih Post, Col Siagian is using tactics similar to those he is accused of employing in East Timor.
The Cenderawasih Post quotes him as saying: "If I meet anyone who has enjoyed the facilities that belong to the state, but who still betrays the nation, I honestly will destroy him."
The statement was reportedly made in response to demands by students and youths for a review of Papua's history.
And Rev Socratez Yoman, President of the Communion of Baptist Churches in Papua Province, says it's not merely threats raising concern in the region.
YOMAN: Every corner in West Papua is intelligence, military everywhere from Sarong to Maloka and the military is also increasing here.
HOLLAND: Rev Yoman says the appointment of Col Siagian coupled with the perceived military buildup has intensified the situation in Papua.
YOMAN: "We need help. We need, the people of West Papua need, genuine or peaceful dialogue between Jakarta and West Papua mediated by the international community - especially the United Nations. It is important".
HOLLAND: Reports from Papua suggest on the 6th of July Col Siagian addressed a meeting attended by various militia groups - including the Red and White Militia group which operated in East Timor.
Matthew Jamieson, from the Institute for Papuan Advocacy & Human Rights, believes Indonesia is also relocating troops to Papua who have been serving in other areas that have been scenes of unrest.
JAMIESON: There's been an increase in the numbers of military and police in West Papua since the close of hostilities in Aceh. It's going into a phase where there's ever-increasing numbers of security forces and now Indonesia seems to be spawning civilian militias.
HOLLAND: Although the exact level of Indonesia's armed commitments in Papua is unclear, it's certain the presence of Col Siagian is causing alarm.
JAMIESON: We need people to start taking a stand because if we go down the track of what happened in East Timor we could end up with many people killed. And if Siagian, apparently, by allowing him to, and the other commanders, by allowing them to develop these militias in Papua they will be able to repeat that experience in Timor.
HOLLAND: The Indonesian military was not available for immediate comment. But Indonesia has previously state it is committed to resolving issues in Papua in a peaceful, just and dignified manner. Indonesia has also denied any allegations of human rights abuses.