Chitra Ramaswamy – Human rights activists and church organisations predict that, without international attention and intervention, West Papua is in danger of becoming the next East Timor.

Recent reports from coastal towns and highland areas in West Papua indicate that Enrico Guterres, one of the architects involved in terror activities in East Timor in 1999, is operating in the region, distributing shipments of guns to local militia. Guterres, indicted by the Indonesian court for crimes against humanity, has remained free while he appeals his sentence and has been operating in West Papua for more than a year. It is thought that the campaign, labelled by some as "a slow and steady genocide", is being stepped up.

Often referred to as Irian Jaya, a province of Indonesia, the western half of the island of New Guinea has been fighting for independence and has effectively been under siege for 40 years, unbeknownst to the rest of the world.

In a 1969 referendum known as the Act of Free Choice, overseen and ratified by the UN, West Papua was handed over to Indonesia in what is widely regarded as a sham: the 1,000 representatives who voted under duress were hand-picked by UN-backed Indonesians resulting in a unanimous victory in favour of Indonesian rule. Human rights campaigners and aid workers alike claim that since that date the UN and international community has turned its back on the troubled region.

Official estimates suggest more than 100,000 West Papuans have died though unofficially the figure is believed to be more than 800,000.

Until December 1, 1999 – a date that is covertly celebrated as West Papuan independence day – the raising of the Papuan flag, the red, blue and white Morning Star, was banned and pronounced an act of treason. Prisons across the country continue to hold Papuans – some for up to 25 years – for raising the flag while December 1 continues to be marked by violence as freedom movements are threatened by government-backed paramilitary groups.

Last December two men believed to have led the flag-raising ceremony in the capital, Jayapura, were arrested and charged with treason.

Benny Wenda, 31, is the leader of DeMMAK, the Koteka Tribal Assembly – natives of the Puncak Jaya highland area which is now closed off to foreigners, including aid workers, due to increased violence. In a December 2004 public statement about the violence in Puncak Jaya, Amnesty International called for "urgent and comprehensive action" and reported "extrajudicial executions, attacks by armed groups, widespread destruction of property and the displacement of thousands of local residents, forced to flee into the jungle where they are at risk of illness and starvation."

In 2000 Wenda led his people in a freedom march, raising the Morning Star to commemorate independence day. The Free Papua Movement has been running a campaign of guerrilla warfare against the Indonesian military since 1969. Since the start of the Papuan freedom struggle, every leader has been murdered, most famously Theys Eluay in November 2001 who was tortured and killed by Indonesian troops.

The Indonesian militia discovered Wenda's involvement and he had no choice but to flee into the jungle to escape torture and death. Two years later he returned to meet with the Koteka Tribal Assembly but was arrested on the way. Wenda was charged with attacking a police station though there was no evidence or witnesses and he had to appear in court seven times, during which he was held in prison and repeatedly threatened and tortured. He finally managed to escape and cross the border into Papua New Guinea and from there to the UK where he now lives in Norfolk.

Wenda fears for the Papuan people in the current climate. "I last heard from my people on January 13," he said. "I heard from the president of the Baptist church in Puncak Jaya. He told me the situation is very bad and that it is getting worse and worse. I'm really worried, this is a timebomb waiting to go off.

They have burned 375 villages to the ground, churches, gardens, everything. More than 6,000 people have had to flee from their homes and go into the jungle. The Indonesian military are looking for my people and if they find them, they will kill them. They are already killing them, they are dying in the jungle.

Thirteen military posts have been put up and no one can get into the area. It is difficult for me to hear about what is going on – my people are really suffering."

Wenda says Guterres is mobilising troops throughout West Papua and describes the government-backed operation as "a secret genocide". He believes more than a million West Papuans have died since 1969. He describes the government policy of transmigration, which many believe is a thinly-veiled programme of ethnic cleansing.

"The government has divided West Papua into three provinces and then into 14 districts," he explained. "This is to break up Papuans and divide them into smaller groups so they are easier to control. Then they are moving the military into each area to get rid of remaining West Papuans as well as bringing in more Indonesians all the time."

In the last four years an additional 25,000 troops have arrived in West Papua and more than a million Indonesian migrants have been relocated. It is thought Indonesians will soon outnumber the 1.5 million native Papuans. In some urban areas they are already outnumbered.

Steffen Keulig, chair of the German section of Friends of People Close to Nature, an organisation advocating for tribal peoples, has spent time in West Papua, particularly in Puncak Jaya. "The violence is escalating," he said, "and what we have is a potential East Timor on our hands. For 25 years everyone ignored East Timor until white missionaries and UN workers were killed and then they started paying attention. Let's not allow the same situation to happen in West Papua."

In a historic move, on December 13, 2004, the British government became the first ever to admit that the people of West Papua were forced into Indonesian rule against their will during the Foreign Office Questions in the House of Lords. West Papuans and activists hope this will be a milestone on the road to peace and independence.

But Keulig remains unconvinced that the West will intervene any time soon. "This is a forgotten war, like the one going on in Aceh. Because of the Tsunami people are starting to notice what has been happening there but after a few months aid workers will be forced to leave and people will forget. Also the west has too many vested economical interests in West Papua. There are logging companies, the Freeport mine is there, BP is there, no one wants to rock the boat."

UN spokesman Farhan Haq said the organisation was aware of the humanitarian situation in West Papua and of recent events on the ground but that they couldn't do anything unless the Indonesian government called for their aid. "The UN hasn't dealt much with the situation," Haq said.

"The governments of Papua New Guinea and Indonesia have not taken anything up at an official level. The UN acts with governments to deal with and oversee a variety of issues but the governments in question, in this situation, haven't brought the UN in."