Kel Dummett – Everywhere you go in Papua the message is the same – Merdeka! Merdeka! Freedom! Freedom! This is particularly true today, the anniversary of the 1967 Act of Free Choice, which led to Indonesia's annexation of the former Dutch colony.

This sham vote followed the United States-brokered New York Agreement of 1962, which settled the dispute between the Dutch and Indonesians over who should control Papua (formerly Irian Jaya). The agreement required that a UN-supervised vote of all adult Papuans be held within seven years in an "act of self-determination, to be carried out in accordance with international practice".

But in the end, just 1025 Papuans, hand-picked by Indonesia, and ostensibly representing one million Papuans, voted under severe duress for integration with Indonesia. The UN and the international community then accepted this vote as legitimate.

According to Amnesty International, in the 33 years since, an estimated 100,000 Papuans have been killed or made to disappear by the Indonesian regime. The past 12 months have seen an escalation in military violence, with Papuan leaders especially targeted. This follows repeated warnings from President Megawati Sukarnoputri that separatists would not be tolerated, and threats from the head of the Indonesian military, General Endriartono Sutarto, that the Papuan independence movement would be crushed.

Since November, 2001, four independence leaders have been murdered by the Indonesian military or have died in mysterious circumstances. One is imprisoned in the notorious Abepura jail. The most recent death was that of Chief Yafeth Yelemaken, a highly respected tribal leader from Wamena, who was poisoned in June, two weeks after returning from Bali where he spoke at a forum during the UN's preparatory meeting for the Johannesburg Earth Summit.

Last November, the Papuan Presidium Council chairman, Chief Theys Eluay, was murdered by the soldiers of the army's feared Kopassus force after he met Indonesian military officials for dinner. The soldier thought to be directly responsible has since been arrested, although, as yet, he has not been charged. Eluay had advocated peaceful dialogue rather than violence in his struggle for independence.

Two other Papuan leaders have been poisoned in recent months: Martinus Kambu, from the OPM's civil leadership, who spent 12 years in jail, died mysteriously, believed poisoned; and academic Marcus Warip was poisoned while on a research trip to Marauke.

Benny Wenda, leader of the traditional highland chiefs' council, DEMMAK, has been imprisoned, and reportedly tortured, after being arrested in early June. Other leaders have been threatened, and middle-of-the-night visits by armed police or military are an increasingly regular occurrence.

Recently I travelled to Papua to find out how Papuans feel about the Indonesian takeover of their country and how they feel about the offer of special autonomy which, Indonesia says, will give new freedoms and a greater say in how Papuans are governed.

It is 2.30am and my wife and I are on a flight from Bali, bound for Timika on Papua's south coast. Our first attempt to visit Papua in 1996 occurred soon after a group of European and Indonesian scientists were taken hostage by Papuan resistance fighters, an act resulting in the province's closure.

We tried again in 1998 but a horrific massacre of up to 150 civilians by Indonesian soldiers on the island of Biak led to Indonesian authorities closing the province.

We are met at the tiny airport by Paula Makabori, who works for both ELSHAM – the key Papuan human rights watch and advocacy group – and LAMASA, the council of traditional landowners in the Timika area. Makabori is a well-educated Papuan, fluent in English, and a key advocate in Papua's struggle for justice and self-determination.

Timika is a typical mining town, languishing beside the tailings-devastated Ajkwa River. It serves the world's largest copper and gold mine, jointly operated by US mining company Freeport McMoran and Anglo-Australian mining giant Rio Tinto. Timika is dirty, noisy and typically Indonesian. It used to be coastal rainforest and sago forest. Sago, the fleshy material in the trunk of sago palms, is the staple food for coastal Papuans.

The town has a mixed population of Indonesians – mainly Javanese, Makassans and Moluccans. It also has many local indigenous people: Komoro from the coastal area, Amungme from the highlands, and other displaced tribal groups from the area. In recent years, thousands of Moluccans, mainly from Ambon, have fled to Papua, and especially to Timika, the nearest point of entry, to escape religious violence.

We settle in a hotel and Makabori returns the next morning with Paulus, the smiling coordinator of LAMASA. We are off to inspect the despoiled Ajkwa River, which runs past the town. Paulus doesn't stop at the military security check point at the entrance to Freeport's concession area – he simply beeps, he and Makabori wave, and we drive through.

Since Thom Beanal – local Amungme leader, vice-chairman of the Papuan Presidium Council and a Freeport Commissioner – renegotiated the mine agreement two years ago, LAMASA is a joint owner of the mine. Refusing to stop at checkpoints is a way to assert their rights as joint owners.

The grey tailings from the mine, 100 kilometres upstream in the mountains, spread out almost as far as the eye can see. The tailings are several kilometres wide, many metres deep, and cover thousands of hectares of what was once pristine coastal rainforest, and the traditional hunting and gathering grounds of the Komoro people.

Only from the air can you get a real feel for the expanse of this devastation. A report on the environmental impacts of the mine claims that 40 million tonnes of mine tailings were dumped into the Ajkwa River system in 1996 alone.

The toxic tailings have obliterated the river that once snaked its way from the mountains through rainforest to the Arufura Sea. Now its polluted waters flow through multiple channels in the enormous grey expanse. Nothing grows on the sea of grey rock and sand.

Freeport-RioTinto scientists claim the tailings are not toxic, but still refuse to permit independent testing of the water in the Ajkwa River. Local people, however, tell us that food crops planted in the area only grow for a few months, then die when the roots reach the polluted water. They also claim that plants around the tailings area grow abnormally.

Several times, as we video and photograph the tailings, Freeport security cars pass us on the road built on the grey levy bank that prevents the tailings from spilling across and covering Timika town.

Makabori tells us about the intimidation that Komoro people suffer every day at the hands of Freeport security. It is normal for security personnel to help themselves to their produce as they pass through security check points. Most of Freeport's security is provided by the Indonesian military and the company has spent tens of millions of dollars building facilities for the thousands of troops stationed in the region.

ELSHAM estimates that 2000 Papuans have been killed in the area since the mine began operations in 1976, and a 1995 Australian Council For Overseas Aid report detailed the murders of 37 civilians, as well as beatings, tortures and house burnings, over a period of nine months.

Makabori and Paulus arrive after breakfast the following day to take us to the first of our scheduled meetings. During the next three weeks we plan to meet human rights, women's and environment NGOs, and political, church and traditional leaders, across Papua. At LAMASA's office, 60 men crowd into the bare room. For two hours we listen to their stories, often delivered almost as political speeches, about intimidation during the sham Act of Free Choice, about the continuing Indonesian police and military abuses, and, to a man (there was only one woman) they reject the Indonesian-imposed special autonomy. They tell us they want merdeka – freedom.

One man's comment remains with us after the meeting: "We respect all human beings whether they come from the mountains or the sea and we want other people to respect us as human beings." From LAMASA we go to a much more informal meeting of a women's support group run by Thom Beanal's wife, Betty. No speeches here, they just quietly tell us about the double injustice suffered by women: rapes and assaults by the Indonesian security forces, and domestic violence at the hands of their Papuan husbands. Like other oppressed indigenous peoples around the world, Papuans' family structures and values are being undermined by the policies of a colonising government and the actions of corporations. The women at this meeting, like their men-folk at LAMASA, stress that their number one concern is independence.

We head to the edge of town for a meeting with Mama Yosepha's YAHAMAK group, set up to support the victims of Indonesian violence. Mama Yosepha Alomang was awarded a prestigious international environment medal last year for her work defending the environment and supporting the victims of military violence.

Most of the women are widows, their husbands having been killed by Indonesian security forces. As they start to tell us some of the horrific stories of abuse and intimidation, one tiny old lady sitting near us, shows us the stump of her leg, which she tells us was shot off by an Indonesian soldier in December, 2000.

We wonder what sort of security threat this old lady had posed. During the next three weeks we hear similar stories of atrocities and abuses everywhere we travel. On the day we flew out of Papua, a US delegation was flying in for talks with political leaders, government officials and NGOs. Hopes were high among Papuans that the US delegation might be going to offer something tangible in the way of justice, or even a path to a genuine act of self-determination. Thom Beanal speculated that the delegation might be coming to discuss security arrangements for US investments in the face of the build-up of Jihad militias in Papua.

At the meeting the US ambassador quickly dashed Papuan hopes by reaffirming America's continuing support for Indonesian sovereignty over Papua, and urging Papuans to accept special autonomy.

In Timika the delegation met representatives from LAMASA and YAHAMAK and tried to convince them that they were getting a fair deal from Freeport. They cited the recent construction of new houses, a school and a hospital as examples of this.

The Papuans pointed out that these facilities were built with their 1 per cent royalties, not from Freeport's profit.

[Kel Dummett is a Melbourne writer.]