The Indonesian government has rejected complaints by human rights activists who say the military is being lenient towards a group of soldiers who tortured two Papuan men last year.

The torture of the men was captured in a chilling video which was shown around the world.

Soldiers took a burning stick to the genitals of one man, who was bound and naked, and they held a hunting knife to the face of another.

They have been charged with disobeying an order to treat prisoners with respect, not with torture.

While the maximum penalty is two-and-a-half years in prison, the most the prosecutors have sought is one year.

Despite complaints from human rights activists, foreign ministry spokesman Michael Tene says the case has been handled appropriately.

"This shows that the Indonesian government is serious in dealing with cases such as this, which is not in line with our own regulations and law," he said.

The soldiers will be sentenced next week.

The case is being closely watched by Indonesia's foreign military allies, including Australia and the US, who view it as a test of Indonesia's commitment to uphold human rights.

The incident occurred in an area of Papua where Indonesian troops frequently clash with poorly armed separatist rebels from the indigenous Melanesian majority.

The video attracted international scrutiny because it recorded the torture in graphic detail.

It later emerged that the military had failed to investigate the incident thoroughly.

Instead it prosecuted a group of soldiers for a separate, less severe case of video-documented torture.

The military said it could not prosecute those responsible because it could not find witnesses and no-one would confess.

It also refused to allow human rights investigators to question the junior soldiers stationed in the area.

Indonesia's president Susilo Bambang Yudhoyono has told a meeting of military and police commanders that they must continue to uphold human rights.

He says that while abuse in Papua is small in scale, it has harmed Indonesia because the government had to spend time explaining the case internationally.