David Usborne, New York – Sitting in the Deluxe Cafe on Broadway just south of Columbia University on the Upper West Side of Manhattan, John Rumbiak is far from his native land. Home is West Papua, a province of Indonesia the size of France which has suffered violence for nearly forty years.

And it seems set to become worse. Rumbiak belongs to one of the indigenous groups who inhabited Papua before the Indonesians arrived. His people are from Biak, an island just off the coast of Papua, which is home to some of the most remote tribes in the world except for Brazil. The tribal leader says that West Papua, formerly Irian Jaya, is in, "a life or death situation".

Rumbiak, now teaching at Columbia, is the head of an indigenous human rights coalition in West Papua called the Institute for Human Rights Study and Advocacy (ELSHAM). Its mission is peace for the province, which has been fighting for freedom since 1962 when its former colonial masters the Netherlands ceded it to Indonesian control.

Human rights observers calculate that the Indonesian military's tactics to suppress independence have taken no fewer than 100,000 civilian lives. It has been compounded by the avarice of foreign firms for lumber and minerals.

West Papua occupies the western half of New Guinea, the eastern end is independent Papua New Guinea. With only 0.01 per cent of the world's population, it is home to 15 per cent of the planet's known languages. It also has an abundance of lumber, copper and gold.

When the Dutch surrendered West Papua to Indonesia it was on the understanding that there would be a referendum on independence. But the vote in 1969, was fixed by the Indonesian authorities. The result left West Papua in Indonesian hands.

Frustration spawned an armed independence group called the Organisasi Papua Merdeka (OPM, or the Free Papua Movement). The Indonesian military was brutal in its response.

Meanwhile, Jakarta, with support from the World Bank, set up a transmigration policy, encouraging different ethnic groups from other islands in the Indonesian archipelago to settle in West Papua. The aim was to rob the indigenous peoples of political and economic control.

Meanwhile, foreign companies were invited to draw wealth from the land. Most infamous has been the American mining company, Freeport McMoRan and Rio Tinto which extracts gold and copper. A recent study by Yale University alleged that the "Indonesian government has shown a callous disregard for the basic human dignity of the people of West Papua".

Human rights group Survival International, one of the organisations being supported by The Independent's Christmas Appeal, assisted local people in blocking plans for a Scott Paper pulp mill. It threatened serious environmental harm. Survival was also among the groups that managed to persuade the World Bank to stop funding transmigration.

Tensions eased somewhat after Indonesia's President Suharto was ousted from power in 1998. In 2001, West Papua was offered political autonomy and an increased share of mining revenues. But the government of President Megawati Sukarnoputri has changed direction. It is moving to divide West Papua into three provinces, apparently to weaken the pro-independence movement.

The fact that East Timor finally did break away after bloodshed and international intervention, in 1999 does not bode well for West Papua. "The independence of East Timor has produced a fear ...," Rumbiak explains. "They are not going to let any other parts of the country follow East Timor."

It is the violent precursor to independence in East Timor that concerns him. This year has seen Timbul Silaen become West Papua's new police chief – the same job that he held in East Timor during its bloody independence drive. (Silaen has recently sued Rumbiak and ELSHAM for allegations it made about recent killings and police involvement.)

More alarming are reports by ELSHAM of the recent arrival in West Papua of Eurico Guterres, the leader of anti-independence militia in East Timor blamed for much bloodshed.

Nor is Rumbiak hopeful that the international community will be able to help. "With the biggest Muslim population in the world, they need Indonesia as a friend," he says. Rumbiak knows he must return to West Papua. But in recent months, he has faced another challenge: threats against his life.