Jo Adetunji – The Indonesian government today confirmed that a graphic video showing scenes of torture by Indonesian soldiers on native Papuans was authentic and said the soldiers involved had been "unprofessional".

The 10-minute video shows footage, apparently filmed on a mobile phone, of two tribal Papuan men from the Puncak Jaya region being tortured. In one scene a naked elderly man appears to be suffocated with an object held over his face while his arms are secured behind his back and his legs tied together.

In one of the most disturbing scenes, omitted from the edited version of the video, the man is shown having a plastic bag forced over his head and screaming in pain as a burning stick is held to his genitals. He is repeatedly interrogated over the location of a weapons cache despite protesting he is a civilian.

Another younger man is paraded before the camera as one of the perpetrators holds a knife underneath various parts of his face including his lips and throat.

While the younger man has been released, the older man's fate is still unknown. Reports suggest he is still missing.

The video comes as the US faces pressure to cease funding for the training of an Indonesian police unit that has been accused of torture in the Maluku province.

The Indonesian government admitted the video, which is believed to have been taken in May, was genuine, after initially claiming it to be a fake. After the footage surfaced the Indonesian government said it would investigate but members voiced suspicions that the video might be part of a separatist campaign to put pressure on them. But today the government confirmed its authenticity and said the soldiers involved had been "unprofessional".

The security affairs minister, Djoko Suyanto, said: "Based on our preliminary report, we found that soldiers on the ground overreacted in handling those people who had been arrested. What they did was unprofessional."

There has been conflict since the Indonesian military moved into the area in 1963. Two years earlier people in the province, a former Dutch colony, had believed it would gain independence and created its own identity as West Papua, though these efforts were thwarted and the Indonesians have continued to lay claim to the area. Survival International said military operations in the area were routine where villages were burned and people forced to flee into the forest. It said a conservative estimate would put the number of deaths caused as a result of the conflict at around 100,000.

Sophie Grig, a campaigner for Survival, said there had been common accounts of soldiers taking footage of atrocities.

"It's not a surprise to us. I met one priest who said soldiers had come to their village and committed rape and had taken a video which had been shown around. This kind of trophy taking, usually with photographs, is commonplace. It's just a relief that it has got out because this has been going on a long time."

Grig said that although the separatists from the Free Papua Movement (OPM) had shown "low-level" resistance in the highland area, the response by the Indonesian military had been "completely disproportional" and was linked to valuable resources.

"The continuing human rights violations are in part a response to a low-level separatist movement and although they have some stolen weapons, they mainly use bows and arrows... The area has the biggest copper and gold mine in the world and the biggest gold reserve up in the hills. It generates a huge amount of tax. Indonesia wants to keep a hold for financial and political reasons and while the government has tried to reign in the military they gains funding from the area and they need to justify their presence."

Survival said military operations were routinely mounted in the area.

Benny Wenda, a Papuan exile living in the UK, said he had come across many accounts of arrests and abuses while living in Papua and as chair of a tribal assembly, including one incident when his brother had kerosene poured on his head and set alight.

"Many Papuans have been through this kind of thing, mainly people in the west and tribal highlands. We want to tell the world. It's been a very long time," he said.

It is not clear what will now happen to the soldiers involved but Suyanto said they would be dealt with "according to military regulations". He added: "It has attracted public and world attention. We'll settle it properly."