Louise Williams – "These are primitive people," said the Indonesian military officer of the tribespeople of the pristine forests and coastal mangrove swamps of the remote province of Irian Jaya.

"Primitive, no!" snapped back an Irianese highlander in the audience, as the officer launched into a briefing for a recent aid program in the provincial capital, Jayapura. "Old methods are not the same as primitive methods; people have been farming here for thousands of years," said the highlander.

These are familiar murmurings of resentment and misunderstanding in Irian Jaya, where animosity between the indigenous tribespeople and the soldiers and bureaucrats of the central Government in Jakarta, who control their daily lives, runs deep. For decades the Irianese, like other ethnic minorities within the Indonesian archipelago, have complained of being treated like second-class citizens in their own villages.

Over the last 10 days, the cultural insults, the sporadic human-rights abuses by Indonesian troops, the domination of local economies by outsiders, and the forced removal of tribes from their lands for mining and development projects, have erupted into mass demonstrations against Indonesian rule. In a series of protests in major towns and remote mountain settlements, the independence flags of the Free Papua Movement (OPM) were raised and Government buildings occupied. Early on Monday morning Indonesian troops opened fire on hundreds of Irianese on the island of Biak, killing up to seven people and injuring 141. The local military commander said about 700 people, some armed with long, curved traditional knives, refused an order to lower the independence flag flapping over the tiny port, ringed by the bountiful coral atolls and the brilliant turquoise of the Pacific Ocean. The small local military detachment had called in a mobile sea patrol, then opened fire with live and rubber bullets.

"This started off with the mood of reform. People thought now that (President Soeharto has resigned) things could be said, feelings could be expressed without people being shot," said a local Catholic priest, sadly.

The protests in Irian Jaya followed major demonstrations for independence in the contested province of East Timor last month, and human-rights officials have warned that, unless Jakarta revises its treatment of ethnic minorities, the Government could face continuing regional rebellions which threaten the Indonesian state.

Indonesia is a fragile multi-ethnic, multi-religious nation and the domination of the bureaucracy and the armed forces by the majority Muslims from the heavily populated island of Java has led to claims of "Javanese colonialism" in other parts of the country.

"This is a long story." the priest said. "Irian Jaya has been part of Indonesia for more than 30 years. But even from that moment the people felt left out. Now there are so many experiences and resentments, ranging from political restrictions to very basic things like the right to move around and the right to speak up."

Ethnically and culturally, there is a case for independence in Irian Jaya. The Irianese share only the legacy of Dutch colonial rule with the rest of Indonesia. Culturally and racially they are distinct, and their natural links lie not with the Javanese Muslims who dominate the Indonesian Government, but with the Melanesian people of the adjoining independent nation of Papua New Guinea. The indigenous people of Irian Jaya have little in common with the people they call the "straight, black hairs", the Malays from Indonesia's populous western islands. The Irian Jayans revere pigs and many are Christians. The majority of Malay Indonesians are Muslims who shun pork and are offended by nakedness.

But the legal case for independence is weak. Unlike East Timor, Irian Jaya's incorporation into Indonesia is recognised internationally, despite criticism from the United States and other Western nations of Indonesia's heavy-handed administration.

Irian Jaya was formally incorporated into Indonesia in 1963. In 1945 Indonesian nationalists had declared independence after a long struggle against the Dutch colonial government. But the Dutch resisted calls to leave Irian Jaya, long after they had withdrawn from the rest of Indonesia.

Indonesian troops began infiltrating Irian Jaya in 1962 in an attempt to fan a rebellion against the Dutch. Fearing war, Holland then handed over administration to the United Nations. The UN signed the territory over to Jakarta a year later. In 1969, 1000 representatives of the Irian people voted unanimously to join Indonesia in an "act of free choice" that was widely criticised by the local people and fuelled a fledgling armed independence movement.

Few of the people who raised their independence flags this week have ever fought with the OPM, but it remains a symbol of their resentment. As a guerrilla army, the OPM survives largely because of the harshness of the terrain and the fact that its small bands of tribesmen, many armed only with traditional weapons, have carried out only sporadic attacks on Indonesian targets.

In 1996, OPM rebels kidnapped a groups of Indonesian and foreign natural scientists, provoking a major assault by Indonesian special forces. The giant Freeport copper and gold mine has also been a frequent target.

Human-rights activists say retaliatory moves by Indonesian troops have included the massacres of civilians believed to sympathise with the OPM, and other human-rights abuses. The presence of the OPM has been used to justify the deployment of Indonesian troops in even the most remote mountain villages, where terrible stories are told of killings and summary executions. Daily life is complicated by suspicion between tribespeople and outsiders.

An Indonesian Human Rights Commission member, Clementino Dos Rios Amaral, says there is a moral argument for Irian Jayan independence. "From what I have heard, for more than 30 years human rights have been violated and there has been torture of the Irianese accused of joining the OPM independence movement. I have talked to students who fear there is an ethnic cleansing of the Irian people with all these killings and torture. "The people feel they are not being treated justly. It is now up to the central Government – if it takes a wrong turn, then disintegration will follow."

But this week the commander of the Indonesian Armed Forces, General Wiranto, made it clear that the raising of a flag, other than the Indonesian flag, would be considered a "treacherous" betrayal of the nation. "This is very significant problem for the continuity of the nation. The armed forces cannot tolerate this and will take firm action," he said.

But the local priest says the feelings of the Irian Jayans have been repressed for too long ."The problem should be talked over with the Government officials; the people come without weapons, please let them talk. If this kind of dialogue is refused, I am afraid there could be a lot more violence."

The highlands of Irian Jaya are a place of unimaginable beauty, a pristine land inaccessible by road and untouched by the modern world save for the tiny grass runways hacked out of the trees for the irregular visits by missionary planes.

Here the mountain air is cool and the breeze is sweet. The old men are clothed only in their penis gourds and hug their naked bodies against the cold. Few such isolated places are left on Earth. Irian Jaya was first visited by the Portuguese in the 16th century but much of the rugged highlands, which conceal the world's only tropical glacier, remain uncharted even today.

The tribes of these mountains and valleys had been farming for 9000 years when they were first contacted by outsiders in the late 1930s. But technologically they were still living in the Stone Age, without metal axes, with no written language, without looms to weave, and divided by mountains so sheer that hundreds of different languages had remained locked away in the valleys.

But with no written history, and after a generation of contact with the outside world, the languages and the stories of these ancient tribal cultures may soon be lost forever. When the control of Irian Jaya was handed over to Indonesia, Jakarta began the process of bringing the people into the fold, enforcing the teaching of the national language, Bahasa Indonesia, in all the village schools and discouraging the preservation of local traditions and beliefs. Irian Jaya had no natural cultural links with the Javanese-dominated Indonesian Government, only the artificial borders drawn up by the Dutch in colonial times.

Irian Jaya is rich with natural resources, gold, copper, timber and fertile land, a vast empty eastern treasure trove for the overcrowded islands to the west. Exploiting valuable natural resources such as timber and the world's largest copper mine at Freeport in the south of the province is highly profitable for the Indonesian Government, which Irianese leaders say has returned little to local tribes in the way of compensation.

But the Government argues that it has done much to develop Irian Jaya, providing basic infrastructure, health services and schools. On the drawing board now is a massive dam and hydro-electric project for the north-east, with associated mining, industrial and residential development in what is now a vast tract of virgin forest.

Over the years the Government has helped tens of thousands of "transmigrants" from Java and other islands to settle in Irian Jaya with the promise of two hectares of land apiece, and other outsiders have followed to take advantage of new trade opportunities. Of the 1.9 million people who live in the province, between 750,000 and 850,000 were born outside Irian Jaya, and the non-indigenous population will continue to rise as the central Government targets Irian Jaya as a priority resettlement area. In the capital, Jayapura, 80 per cent of the population are non-indigenous people.

In the mountains, as they have for centuries, the men live in one hut, the women in another with the children and the pigs. It is easy to romanticise the simplicity of a self-sufficient village existence, free from even the intrusion of a radio or a telephone. But in the health clinics the statistics reveal a less appealing reality. Every year scores of people die from disease, children and mothers are lost at birth, entire villages suffer chronic bronchitis because without bedding or warm clothes they must huddle around smoky fires in the huts every night.

It is this "primitiveness" that Indonesian Government officials argue must end. But few people are asking the key question – how to improve the health and quality of life of remote tribal people without destroying the fabric of their society. Already development is reaching these tiny villages, even if only to lure away the young to the towns.

"We have no doctor, no paramedic, only a tiny airstrip," says one health worker. "I see the old people still working here happily, but the young people like to go to the big towns like Wamena or Jayapura."

In Wamena, like many other towns, migrants have come from other parts of Indonesia to control commerce. Even the souvenir shop selling handicrafts from the mountains to the trickle of tourists is run by an outsider. Many young tribesmen move into town to do menial jobs. Alcohol is a growing problem, as is the sale of land for a pittance to outsiders. As village life gradually breaks down, more and more people drift to the edges of the towns.

"The problems are like being in a no-man's land between tradition and modernity; people no longer know where they fit. They don't know how to do business, they can't compete with the outsiders, so they get lost," said one highlander. But they are fighting it. Clementino Dos Rios Amaral says that out of the nine regions in Irian Jaya only two are governed by native Irianese. "That sharpens the feeling that they are being discriminated against."

Local environmentalist Chalid Muhammad says at first he thought all the Irianese wanted was to be treated humanely and fairly and not like second-class citizens. "But now I think they may want more; anti-Indonesian sentiment is intensifying." For the moment Irian Jaya's hopes for independence are slim. But modern Indonesia is a political entity based on an outdated colonial border and some political scientists believe that a weakening of the Jakarta Government could eventually see the Indonesian nation splinter, with new rebellions in the outer islands.