West Papua’s Forever War

Prabowo Subianto first made his name as an Indonesian military leader trying to crush East Timor’s push for independence. Today he is president — and his government is fighting another colonial war in West Papua.

Prabowo Subianto during the inauguration of regional heads at the Presidential Palace in Jakarta, Indonesia, on February 20, 2025. (Bay Ismoyo / AFP via Getty Images)

In September 2024, Susi Air pilot Philip Mehrtens was released after nineteen months in captivity by the West Papuan liberation army and returned to his native New Zealand. Mehrtens’s kidnapping was a personal trauma — and an ordeal for his friends and family. Locally, the central highlands region is notorious for its vast human rights violations, its refugee crisis, and blatant colonial warfare. For the liberation movement, Mehrtens’s presence was an opportunity.

One source attached to a local refugee-aid program in Nduga Regency tells me that “when Mehrtens was still in the highlands, there was attention on the conflict.”  She adds that “a white man walked among the Papuans, in captivity, sure, but he walked on the same soil and along the same paths as the refugees, the suffering people, and the liberation movement.”  Surely, “people feel sorry for him, and rightly so; he couldn’t return to his loved ones. But in the same vein, Mehrtens’s case forced many to think about us who live here, who also wish to go somewhere — to freedom, to independence, to have our lives back.”

As Mehrtens left West Papua via a press frenzy in Jakarta, so did Western media. Their focus turned elsewhere. This is, after all, also a time of daily human rights atrocities in out-starved and aid-blockaded Gaza, the besieged and US-raided Yemen, and in Ukraine.

Mehrtens was released near Yuguru, one of numerous villages in in Nduga that have turned into last resorts for internally displaced people (IDPs), due to the armed conflict that erupted in late 2018. Then, the West Papua National Liberation Army (TPNPB-OPM) attacked a frontier site for the construction site of Trans Papua, a mega-road project that, when completed, will have brought 4,325 kilometers (2,685 miles) of paved road to West Papua. The deadly attack against Indonesian road workers opened the door for Indonesia’s largest military operation since its occupation of East Timor in 1975. Despite the alleged use of chemical warfare, massive air raids, and the installation of thousands of soldiers at remote army stations, TPNPB-OPM has continued its armed resistance.

Mehrtens’s kidnapping was also a major embarrassment for the political elite in Jakarta, and a sign of the military’s failure to “secure” and “pacify” West Papua by armed force. Shortly after his release, Indonesia’s newly elected president, Prabowo Subianto, assumed office, having been elected on a demagogic nationalist agenda. He had secured nearly 60 percent of the vote, aided by the fact that his running mate, Gibran Rakabuming Raka, happened to be the son of his predecessor, the vastly popular Joko “Jokowi” Widodo.

Since taking office, Prabowo has “increased the use of excessive violence and force,” according to Theo Hesegem, a human rights defender. “The violence in West Papua’s central highlands has increased greatly,” he tells me.

Even worse, he adds, the increased deployments of thousands of military personnel grew beyond the president’s control, paving the way for isolated army units to commit atrocities and human rights crimes against unarmed and unprotected civilians without any risk of legal punishment. Shortly after Mehrtens’s release, “a silent TNI [Indonesian military] operation” swept through Yuguru, and a suspected independence activist, twenty-seven-year-old Abral Wandikbo, was kidnapped, killed, mutilated, and later found dead in a community plantation area.

Reports from various isolated areas in the central highlands have proven to Hesegem that kidnappings, summary executions, and mutilations are “part of a pattern of TNI’s working methods” in West Papua, and that the tragic fate of Abral Wandikbo is merely one of many in this region. Witnesses have provided accounts and photo documentation of mutilated ears, mouths, noses, and testicles: crimes inflicted upon civilians by TNI units sweeping through refugee communities shortly after massive air raids initiated by the Jakarta government.

“The military apparatus doesn’t distinguish between civilians and the TPNPB-OPM,” says Hesegem.

West Papua remains an enclosed conflict zone, off-limits for the United Nations High Commissioner for Refugees, international human rights groups, independent journalists, and humanitarian aid organizations. Instead, local church missions and poorly equipped regional administrations must cope with an alarming crisis of hunger, lacking health care facilities, and between 60,000 and 100,000 IDPs according to the Office of the United Nations High Commissioner for Human Rights. “There’s absolutely no end in sight for the IDPs,” Hesegem tells me.

Since 2018, when the ongoing armed conflict between the liberation army and Indonesian military forces broke out in earnest, countless civilians have died either due to bullets, bomb raids, hunger, or diseases. “For seven years, many refugees have died because there’s no health care for them,” he adds. A growing number of West Papuan activists and international human rights scholars label Indonesia’s ill-treatment of civilians a “slow-motion genocide.”

First, Hesegem underlines, you ought to understand the long-term impact of today’s colonialism. Neither health care nor education facilities prepare the young generation in the central highlands for the future — a tomorrow whose outlook remains unclear due to persistent Indonesian military operations in search of the ill-armed but mobile liberation movement, whose strongholds are found in the mountains and thick forests of interior West Papua.

Second, West Papua looks set to be eternally colonized by Indonesia, after Jakarta’s dismissal of the West Papuan liberation movements’ request to arrange for a UN-led referendum on the future status of the western part of New Guinea. In 1969, after Indonesia’s initial military annexation of West Papua, a blatantly corrupt UN-led referendum called the Act of Free Choice clinched Jakarta’s control over the resourceful territory. Indonesian control over West Papua has brought fortunes to investors and companies involved in oil palm production, copper and iron mining, and the forestry business. Yet, it has spelled social, cultural, and environmental disaster for civilians. The Freeport Mine, one of Indonesia’s most valuable sources of income, has polluted rivers, soils, and lakes.

The Trans Papua project is expected to seal West Papua’s fate as an Indonesian project, helping the central government to deal with concerns around overpopulation in Java, Sumatra, and Sulawesi through large-scale so-called transmigration programs. These continue to loot public and community lands in West Papua that are handed over to settlers, providing land titles to have-nots in other parts of the Indonesian archipelago, but also turning West Papuan civilians into second-class citizens in their own land.

According to regional and local policymakers, among them Indonesians born and raised in West Papua, the Trans Papua project is deemed a necessary evil to bring development, jobs, and necessary social and political infrastructure to isolated pockets of ”eastern Indonesia.” One source of mine — an Indonesian politician in the West Papuan capital Jayapura and a champion of Trans Papua — considers the project “part of a sustainable, humane, and civilizing development of Papua.”

In his view, the road isn’t merely a massive investment in physical infrastructure, it is also a long-term investment in “social defense,” where “modernity and capitalism will protect the Papuans from themselves, from their Stone Age living traditions.”

This source, however, deems Jakarta’s institutionalized “use of violence” against social upheavals as a sign of weakness and of a lack of understanding for the civilian population’s request for political and social involvement in the development of West Papua. “It’s an endless dilemma,” he says. “The government simply cannot respond to security and order issues with only a security mindset. We all need to consider ourselves as citizens of the Republic of Indonesia. If that’s not the case, it will only produce endless resistance, whatever development project is being carried out.”

However benevolent Indonesian policymakers’ intentions may be, they simply haven’t provided West Papuans with any financial stability or sense of belonging to a larger national identity.

Instead, riches of natural resources such as copper, ore, gold, timber, and fishing have made fortunes elsewhere, leaving behind a deforested and paved-over island. This economic takeover underlines the claims of an ongoing ”silent genocide,” as stated in a 2013 Sydney University report, and echoed by Benny Wenda, a West Papuan independence leader in exile in London, who links West Papua’s ordeals to Indonesia’s quarter-century-long occupation of East Timor. This illegal, US-supported occupation sprang from the large-scale invasion that followed Timorese independence from Portugal in 1975, and the occupation was led by Indonesia’s then defense minister and current president, Prabowo.

In the 1980s, he toured East Timor along with special-forces units, and various witnesses have accused him of committing atrocities while there. Aside from Prabowo’s human rights crimes in East Timor and responsibility for the ongoing atrocities in West Papua, he is deemed responsible for the deaths of various civilians in Java in 1998, during the collapse of the regime of his father-in-law, the dictator Suharto.

It may seem ironic that Prabowo — tainted by the documented bloodshed of minority groups, democracy advocates, West Papuan and Timorese independence activists — secured legal political power via the same democratic system that he fought so hard to crush as an integral player in Suharto’s “New Order” regime (1967–98). His success is rooted in the support of a young generation, “poorly informed of the country’s past under a military dictatorship,” as the BBC’s Frances Mao reported after his election victory.

Prabowo’s rise to Indonesia’s highest political office reflects a worldwide authoritarian push, directed by far-right nationalism. In the United States, Donald Trump’s return to office marks the onset of what Naomi Klein and Astra Taylor call an “end times fascism,” while in 2022, Italy marked a century since Benito Mussolini’s March on Rome by swearing in its first prime minister from a party of neofascist roots.

In Southeast Asia, Prabowo isn’t the only political blast from the past. In the Philippines, Ferdinand “Bongbong” Marcos Jr showed the world that being the son of a notorious dictator and kleptocrat can slam open the doors into the highest political office. Bongbong won the presidency in a landslide in 2022, and like Prabowo leaned on a vice president, Sara Duterte, who also happened to be the child of a former president, Rodrigo Duterte.

In the end, resolution to the grave human rights situation in West Papua doesn’t depend merely on a sincere and humanistic wake-up call among the political elite and financial quarters in Jakarta. It also comes down to the commitment of the international community, which ever since the 1960s has merely ignored the systematic plunder of West Papua’s natural resources at the expanse of the civilian population.

As a West Papuan civilian tells me (she wished to remain anonymous), “We’re being annihilated,” she says. “It’s clear that the Indonesians see no place for us here. They want us to vanish, die, or just leave. But where can we go? This is our land.”

Hesegem keeps documenting Indonesia’s vast human rights crimes in the central highlands and remains a vital source of information for the world outside of West Papua. In Nduga, near the village of Yuguru, where IDPs settled after the outbreak of the armed conflict in late 2018, TNI continues to sweep the area in search of the kidnappers and those responsible for the kidnapping of the New Zealander Mehrtens.

“TNI operates within the frame of so-called ‘silent operations,’” says Hesegem. “In Yuguru, they continue to occur. The trauma inflicted upon civilians is massive. There is no freedom for the community to live in their land, not even as IDPs.” As wars in the Middle East and Ukraine dominate global media headlines, West Papua’s attempt to muster international momentum for its quest for independence faces an ever-tougher picture.