Indonesia has admitted its soldiers tortured a Papuan man whose ordeal was captured on video and posted on the internet.

Indonesian security affairs minister Djoko Suyanto says a preliminary investigation has found Indonesian soldiers were responsible for the abuse.

The video shows them repeatedly prodding one Papuan man's genitals with a burning stick as he screams in fear and agony, and holding a hunting knife to the face of another.

The minister says the soldiers "overreacted" in handling the men, who were suspected of knowing the location of a separatist weapons cache.

"Based on our preliminary report, we found that soldiers on the ground overreacted in handling those people who had been arrested," he said.

"What they did was unprofessional."

Human rights activists have called for an independent investigation, but the minister says the soldiers will be dealt with "according to military regulations".

"It has attracted public and world attention. We'll settle it properly," he said.