A commander of a Papuan militant group who had half his leg amputated because of a gunshot wound has vowed to return to the jungle to fight against Indonesian rule.

Speaking from a rebel training camp just inside the Papua New Guinean border, Danny Kogoya says he was unarmed and surrendering when police shot him below the knee last year.

Indonesian police say he was resisting arrest.

Now at his PNG hideout, known as Camp Victoria, Mr Kogoya's fellow rebels are holding a small show of arms.

Displaying homemade rifles, bows and arrows and with some wearing ceremonial headdresses and shell necklaces, they rally around the Morning Star flag - the symbol of West Papuan independence that is banned in Indonesia.

They have no bullets but they say they want to fight the Indonesians.

For almost 50 years the Free Papua Movement (OPM) has fought against Indonesia's control of Papua and West Papua province.

Mr Kogoya is a commander for the OPM's militant wing. He says his leg was amputated without his permission while he was jailed on manslaughter charges last year.

"This leg was amputated for the Free Papua Movement. I am asking for independence... I am asking for West Papua to exit the Republic of Indonesia," he said.

After his release from prison, Mr Kogoya says police threatened to re-arrest him, so he fled across the border to Papua New Guinea.

Now, he says he will get the remaining shotgun pellets removed from the stump of his leg, find a prosthetic limb and return to the bush to keep fighting.

Allegations of atrocities hard to verify

Papuan militants display their homemade rifles at Camp Victoria. ( ABC )

Since the 1960s, the armed wing of the Free Papua Movement has conducted a low-level insurgency within Indonesia.

Allegations of atrocities committed by Indonesian forces within Papua and West Papua province are difficult to check because the international media is kept out.

It is also hard to get a real sense of the strength of the West Papuan militants.

Mr Kogoya says he commands a standby army of 7,000 men, with around 200 active fighters, but those figures cannot be verified.

Camp Victoria has played an important role in the history of the West Papuan independence movement.

It has been a training camp, a gateway from Indonesia to Papua New Guinea and a place where rival factions have split and reunited. But what role it will play in the future of the West Papuan struggle is unclear.

PNG signs extradition deal with Indonesia

Last month Papua New Guinea and Indonesia signed an extradition treaty, which PNG's opposition says could be used to target West Papuan activists.

"I think that is the cooperation between the Papua New Guinean and the Indonesian government. That's their issue. Not West Papua. We will keep on fighting until we are independent," he said.

PNG prime minister Peter O'Neill says the extradition treaty will be used for criminals and not political activists, but for those who could be considered both it is yet to be tested.

"We have had a policy that the issue of West Papua is an integral part of Indonesia. We have consistently maintained that," he said.

"But we are encouraged by the invitation by the Indonesian government through the president for the first time in its history to help in managing some of the issues on the ground in West Papua."

Mr Kogoya, meanwhile, is calling for all West Papuan activists living abroad to return to Camp Victoria and continue their struggle.

"I want Jacob Prai in Sweden, John Ondawame in Australia, all those leaders abroad to come back to this camp, Camp Victoria, to continue the struggle for independence," he said.