Rob Taylor in Jakarta – Indonesia's intelligence chief has accused an Australian-backed aid group of being behind clashes in the province of West Papua in which four security officers were killed.

Major-General Syamsir Siregar, who heads the Indonesian State Intelligence Agency, or BIN, refused to name the organisation which he believed fomented last week's protests against the huge US-owned Freeport gold and copper mine. Three policemen and an air force officer were killed in the riots.

But General Siregar said the aid organisation operated in Papua and had close ties with an outside country, which Indonesian newspapers said was Australia.

"There was an NGO (non-government organisation) sponsoring it all," he said according to Koran Tempo newspaper. "As far as I know, the mover was a local NGO, but had connections with the outside. "I guess you all know (who)."

Indonesia has previously accused several Australian aid groups of secretly backing the independence aims of West Papuan separatists, who have for decades waged a low-level insurgency against Jakarta rule.

The aid arm of the Australian union movement, Union Aid Abroad-APHEDA, has come in for particular criticism for circulating communiques from the separatist Papuan Council Presidium to activists in Australia. Many influential Indonesians believe Canberra secretly backs independence for West Papua and hopes for an East Timor-style separation.

In a 2003 meeting with Prime Minister John Howard, former Indonesian president Megawati Sukarnoputri said she was concerned Australian government aid funds were being used indirectly to support separatist movements in Indonesia.

The executive director of APHEDA, Peter Jennings, said the agency had no projects in Papua. But he believed the West Papuan people had been denied their rights in a 1969 UN integration referendum widely regarded as a sham. "The bottom line is the people of West Papua are entitled to another UN-sponsored referendum on their future," he told AAP.

The Australian Government's aid wing, Ausaid, warns NGOs it will not approve funding for projects which "subsidise evangelism or missionary outreach, or similar activities by partisan political organisations". It also warns it will not support independence movements.

In February, Foreign Minister Alexander Downer assured Jakarta that Australia believed West Papua should remain a part of Indonesia. That assurance was given after 43 West Papuans landed in Australia's north seeking asylum.

Following last week's clash in West Papua's provincial capital, Jayapura, police have arrested 14 people and questioned more than 70 students on charges ranging from destruction of property to assault and murder.