The United Liberation Movement for West Papua is calling for mining company Freeport to stop operating in Papua until local conflict ceases.
Violent clashes have broken out between Indonesian security forces and the West Papua National Liberation Army near the Freeport gold and copper mine.
The Liberation Army has claimed responsibility for the shooting deaths of an Indonesian soldier and a policeman in the Freeport area since late last month.
It also said it had injured several police while it targeted the lucrative mine as a symbol of the Indonesian state it had declared war against.
The Liberation Movement chair, Benny Wenda, said Papuan military fighters had a right to defend ancestral lands against an invading force.
Mr Wenda accused Freeport of providing support to Indonesian forces to carry out mass killings, and depopulate local villages. Freeport should stop operating in West Papua until bloodshed ceased, he said.
"Freeport has long been the single largest tax payer to the Indonesian colonial state, taxes which are used to buy the weapons which kill my people," Mr Wenda said in a statement.
"There have always been West Papuans who, with the support of the people, defend themselves, their mountains and their forests. They are the West Papuan home guard.
"The people of West Papua have lived on their lands for tens of thousands of years. Until Indonesia came there was no mass killing, deforestation or pollution. Now, our land is a hunting ground for the Indonesian military."
Papua region police chief Paulus Waterpauw has told local media that security forces are looking to arrest members of the West Papua Liberation Army which has been staging ambush attacks on his personnel.
PT Freeport has warned its employees in Papua about heightened security risks in the area, advising them to stay vigilant.
Meanwhile, the New York Times reports that almost 2000 West Papuan villagers have fled the area due to the shootouts between the Liberation Army's guerilla fights and Indonesian forces.
A local disaster mitigation agency chief, Yosias Lossu, said buses owned by PT Freeport Indonesia evacuated about 1000 villagers, mostly women and children, since last week.
Another 800 villagers were evacuated with assistance of police last Friday, he said.