Indonesia's military claims it now controls all of Aceh province, six weeks after imposing martial law to crush separatist rebels. But local human rights groups are counting the civilian cost of the war... saying as many as 35-thousand Acehenese have fled their homes and hundreds more have been killed in attacks and air raids.

Presenter/Interviewer: Tricia Fitzgerald

Speakers: Doctor Hasbullah Saad, Indonesia's National Human Rights Commission KOMNAS-HAM

Fitzgerald: The picture emerging from the war in Aceh is confirming the worst fears of human rights groups. The progress made under the six month-long ceasefire has gone up in smoke in just six weeks of war. Hundreds of civilians have been killed or arrested or have simply disappeared since the military offensive began.

A new report complied by a human rights group who asked to remain anonymous due to fears for their family's safety shows children, teachers and human rights workers are amongst those killed or detained in the conflict.

Human rights group: In the past six weeks of martial law over 400 civilians, including 19 children and seven school teachers have been killed. Almost 300 civilians have been arrested or have disappeared, including nine human rights and Red Cross activists. Two-thousand school buildings have been burned to the ground and over 100 homes have been destroyed.

Fitzgerald: Doctor Hasbullah Saad of Indonesia's peak human rights group Komnas-HAM, the National Human Rights Commission, says thousands of civilians are being caught unawares when the conflict and chaos of the war suddenly moves into their villages.

Saad: You know everybody well they fear to be on the ground because suddenly the conflict will come and unexpected and nobody can tell when and where, and suddenly the conflict, comes rise very much and kills a lot of people. Civilians they fear to be in their village and home, and a lot of them moved to be IDP's [internally displaced persons] ... staying in school building or mosque building or other public building because they're so worried to stay in their own house and their village.

Fitzgerald: The latest high profile civilian victim of the war is Muhammad Nazar, the leader of Aceh's Information for a Referendum Centre. He's been given a five-year jail term for sedition for calling for Acehanese to be allowed to have a referendum on self-rule.

Three Indonesian journalists covering the conflict have also become victims with one found dead floating in a river and another two missing in a conflict area.

The local human rights group mentioned earlier says even civilians who've fled into refugee camps aren't safe. Its report says camps established spontaneously or by the military have been targeted by Indonesian soldiers who are removing civilians for interrogation or abuse.

Human rights group: Even in the refugee camps civilians are not safe. In the past two weeks alone the TNI and Brimob have taken two to three girls from the camps at night and if they are returned they are in a miserable condition having been raped. Overall over 100 women and teenagers have been raped.

Fitzgerald: The National Human Rights Commission says it's investigating reports of three mass gravesites involving at least a dozen bodies. It says the military has come under fire for excavating the sites without independent forensic back-up.

Saad: You know a lot of mass graves now was dug by TNI but certain NGO protests about the way of they dig the mass graves without any forensic back-up you know. I hear that TNI and police ask the forensic from North Sumatra to be there but during the digging process not any forensic there. Certain NGOs protested because this is the same as destroying the evidence.

Fitzgerald: Investigating human rights abuses in this conflict has become dangerous and almost impossible. The Commission is compiling a report to present to the Minister of Security and Political Affairs.

Doctor Saad says the report will contain complaints about the lack of protection for human rights workers on the ground in Aceh, but he adds that the relationship between the Commission and the military is already strained.

Saad: Martial law makes it very, very clear, it means there's no protection for the humanitarian workers, for the human rights workers on the ground. And that's why the commission send the mission to Minister for Political and Security Affairs to discuss about each [other's] position, human rights, the commission position and TNI position, in order to make more better understanding [with] each other, and reduce the mis-understanding and conflicts between TNI and KOMNAS HAM.