BANGKOK — It has been 59 years since separatists in the Indonesian territory of West Papua raised their red, white and blue flag and declared independence. The region has been in conflict ever since.

This month, the United Nations Human Rights Office called on all sides to reduce escalating violence in the territory, which has included the recent killings of activists, church workers and members of Indonesian security forces.

At the same time, a rebel leader living overseas announced that he had been elected interim president of the embattled region in hopes of unifying the movement seeking independence from Indonesia, known as the Free Papua Movement.

Benny Wenda, who escaped from an Indonesian jail 18 years ago and later received political asylum in Britain, declared himself head of West Papua’s first government-in-exile on Dec. 1, the anniversary of the independence declaration. Already, one armed group in West Papua has said it doesn’t recognize his authority.

Mr. Wenda claimed he was elected by a clandestine congress that met in secret. He said Papuans are victims of a slow-moving genocide that will not end until the territory gains its freedom from Indonesia.

“Our independent nation was stolen in 1963 by the Indonesian government,” he said by phone from Oxford. “We are taking another step toward reclaiming our legal and moral rights.”

Indonesia has no intention of granting independence to the two provinces that make up West Papua. The country’s minister for political, legal and security affairs, Mohammad Mahfud MD, rejected the idea that Mr. Wenda could ever represent the Papuan people.

“He’s a rebel. He’s an outsider,” the minister told reporters. “He is stateless. In England he is a guest. In Indonesia his citizenship has been revoked. So how does he lead a country?”

Indigenous people under pressure.

The ongoing conflict in West Papua has largely been overlooked by the outside world. In recent years, the government has limited access by foreign journalists, researchers and United Nations rights officials.

West Papua is also one of the most isolated and undeveloped parts of the world. Home to about four million people, it takes up the western half of New Guinea — the world’s second-biggest island after Greenland — and is split into two large provinces, confusingly named Papua and West Papua. The island’s eastern half is occupied by the nation of Papua New Guinea.

The people of West Papua are divided into more than 250 tribes with more than 400 languages. Demographic data is scarce, but a steady influx of migrants from other islands means that Indigenous Papuans are likely now outnumbered.

Native Papuans have dark skin and curly hair and regularly face racism and discrimination. Violent clashes erupted last year after reports emerged of the police insulting students with racist slurs.

Commerce in cities and towns is dominated by non-Papuans while many Indigenous Papuans eke out a subsistence living in the region’s highlands, where many villages are accessible only on foot. The Indigenous people have among the country’s lowest life expectancies and infant mortality is high.

Mr. Mahfud, the security affairs minister, acknowledged that the government had not done enough to help Indigenous Papuans and that corrupt local officials had siphoned off money earmarked for Indigenous communities.

“We have prepared a presidential decree that is now being studied so that development in Papua can truly be felt by the people,” he said. “The budget for Papua is huge, but it is corrupted by the elites there so it does not reach the people.”

Annexed by Indonesia, separatists dream of independence.

Separatists have waged a low-key insurgency for decades in a quest for self-rule. Calling for independence in West Papua is considered treason under Indonesian law, and raising the independence flag can bring a prison sentence of up to 15 years.

Two years after Papuans declared independence in 1961, Indonesia sent troops to occupy the former Dutch territory, and has maintained a military presence ever since. In 1969, in a vote regarded by many Papuans as rigged, Indonesia rounded up a thousand tribal leaders and held them until they agreed to join Indonesia.

The result was called “The Act of Free Choice,” and, after ratification by the United Nations, became Indonesia’s legal foundation for controlling West Papua. Many Papuans see their region as occupied and would like a true referendum to decide its status.

“Most Papuans want to be free,” said Veronica Koman, an Indonesian human rights attorney and activist based in Australia. “They want independence from Indonesia. They want a referendum. It is fair for everyone.”

The Indonesian government adamantly opposes holding a vote.

“The referendum was in November 1969,” Mr. Mahfud said. “It was ratified by the U.N. General Assembly that Papua is a legitimate part of Indonesia. Therefore, there will be no more. It is impossible for the U.N. to make a decision twice on the same matter.”

A land rich in natural resources.

West Papua is rich in natural resources, giving Indonesia a strong incentive not to let it go. As outsiders come to the province to help exploit its resources, Native Papuans complain of a lack of jobs and opportunity.

The mountainous island, which lies north of Australia, has the world’s second-largest rainforest after the Amazon and is rich in biodiversity, with plant and animal species that remain unknown to the outside world.

Indonesia has harvested West Papua’s wealth in minerals, natural gas and timber with the help of foreign companies. The American mining company Freeport-McMoRan extracted gold and copper for decades from the giant Grasberg mine. An international consortium led by BP operates the huge Tangguh natural gas field.

Other companies are logging large swaths of pristine forest and replacing them with lucrative palm oil plantations. West Papua’s forests, home to some of the country’s rarest birds, are also prime hunting grounds for illegal poachers. A bird of paradise can fetch as much as $1,500 on the black market in Jakarta.

In the coming years, wilderness areas will be opened up even more by a 2,700-mile trans-Papuan highway now under construction, accelerating the extraction of resources, both legal and illegal.

Escalating violence as more troops arrive.

Violence has been escalating since December 2018, when 19 migrant laborers working on the Trans-Papua Highway were killed by Papuan rebels.

The government has deployed growing numbers of soldiers and police officers in West Papua, but the total number stationed there remains classified.

“We urge the government of Indonesia to uphold people’s rights to freedom of expression, peaceful assembly and association in line with its international obligations,” said Ravina Shamdasani, a spokeswoman for the United Nations Human Rights Office in Geneva.

Amnesty International has identified 38 prisoners of conscience in West Papua, more than the rest of Indonesia combined. The group says most are charged with treason for the peaceful and legitimate expression of their views.

Another human rights group, Human Rights and Peace in Papua, said last week that as many 60,000 Papuans had been displaced by recent fighting.

Faced with such conditions, Ms. Koman, the activist, said desperate young people have joined rebel groups in the jungle. “This vicious cycle of violence needs to be stopped to save the young generation of Papuans,” she said. “They will end up in jail or fighting and sacrificing their lives.”

Papua’s independence movement has long been fragmented and it is unclear how much support Mr. Wenda has for his claim to be president.

Six years ago, three factions united behind Mr. Wenda to form the United Liberation Movement for West Papua, and Mr. Wenda says he has their backing. But one armed group, the National Liberation Army of West Papua-Free Papua Organization, issued a statement rejecting his claim, saying he is a resident of Britain who does not have the majority support of Papuans.

As president of an independent Papua, Mr. Wenda said, he would protect the rights of Indigenous Papuans and halt environmental destruction.

“Our rights have been violated under international law,” he said. “Indonesia destroys not only my people but our forests and our mountains.”

Muktita Suhartono contributed reporting.

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