The family of a one-legged West Papuan rebel who died in Papua New Guinea at the weekend has accused the Indonesian consulate of interfering with his planned autopsy.

The Free Papua Movement (OPM) regional commander Danny Kogoya died on Sunday in the north-west town of Vanimo, where he has been hiding since fleeing the threat of arrest in Indonesia earlier this year.

The cause of his death is not yet clear.

The OPM is a group fighting for West Papuan independence from Indonesia and Danny Kogoya was the group's commander for the Jayapura region.

Mr Kogoya was shot by Indonesian security forces during an arrest last year and later had his leg amputated while in custody.

In July, Mr Kogoya spoke to the ABC after his leg had been amputated, where he vowed to return to the jungle to fight against Indonesian rule.

He told the ABC he was unarmed and surrendering when police shot him below the knee and his leg was amputated without his permission while he was jailed on manslaughter charges.

"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.

At the time Mr Kogoya said he need further surgery to remove bullet fragments from the stump of his leg.

Questions over death

Initial reports blamed infection as the cause of death, but a doctor at Vanimo Hospital says Mr Kogoya was being treated for liver failure when he died.

A spokesman for Danny Kogoya's family, Jeffrey Bomanak, has accused the Indonesian consul-general of interfering with plans to carry out an autopsy at Vanimo Hospital.

He alleges the consul-general, who is based in Vanimo, asked the hospital to not go ahead with the post mortem.

"[The] Indonesian consulate disturbed that process. I don't know what reason, [it's] not clear the reason. Because he wanted to disturb the process about operation, even to check the full report of hospital," Mr Bomanak said.

The ABC has been unable to reach the consulate or the consul-general for comment.

But the emergency department registrar at Vanimo Hospital, Dr Kennan Witari, claims the Indonesian consul-general was involved.

"I'm not really sure why he's following this thing like this, to this extent. But I heard that probably the consulate wants the body for some legal reasons and the family wants the body too, so they're still going to and fro," Dr Kennan Witari said.

Family spokesman Jeffrey Bomanak says he suspects foul play and wants an autopsy to take place in the coming days.

Danny Kogoya's family then wants to take the body back to Jayapura for it to be buried in the same place as his amputated leg.

"Half [his] leg is already planted [buried] there, in West Papua. So we cannot plant [bury] the body here... that is a big wrong," Mr Bomanak said.

Further discussions between Mr Kogoya's family, the Indonesian consulate and the hospital about a post mortem are expected.

Preparations for a funeral or burial have not yet been confirmed.

Decades-old fight

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 confirm 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 told the ABC in July he commanded a standby army of 7,000 men, with around 200 active fighters, but those figures cannot be verified.