What's Really Going On in the Papua Conflict?

Even on the broad spectrum of under-reported, under-acknowledged, and outright ignored conflicts, the insurgency in Indonesia’s Papua region is in a category all its own. Fought since 1962, with a total death toll estimated to be as high as 300,000 or more, the conflict is all but absent from global politics and media.

The nation of Indonesia, condemned by the United Nations as recently as 2022 for the “shocking abuses” ongoing in the region, faces hardly any repercussions for its conduct, even as the nation’s new leader promises a renewed counterinsurgent focus on Papuan soil. Today, Indonesia maintains a known, repressive, and egregiously violent police state, on the western half of the Papua landmass, but the conflict is a locked box. Very few international observers get in, and precious little news gets out.

Right now, based on the minimal, scattered reporting that makes its way to global audiences, the violence in the Papua region is accelerating. Thousands of Indonesian troops are streaming into the territory, Free Papuan insurgents are turning to increasingly desperate tactics, and an untold number of people have been killed, injured, or displaced.

But from the outside, looking in, it would seem as if there were no conflict in the Papua region at all.

Hell in the Highlands.

The island of Papua is a complex and historically fraught place, split in two today between Indonesia and Papua New Guinea, and bearing deep scars of imperial expansion and colonial exploitation. Since it gained sovereignty, Indonesia has insisted on maintaining its claim to the western half of Papua and its outlying islands, as the rightful successor to the Dutch East Indies and the inheritor of its former borders.

Papuans, however, have been split on the idea of Indonesian rule since before Indonesia was a sovereign nation. Some have been open to the concept, others attempted to seek continued protection from the Dutch, and still others attempted to pursue independence or unification with Papua New Guinea. After the departure of the Dutch in 1962, and the end of a transitional period under United Nations oversight in 1963, West Papua has been internationally recognized as part of Indonesia, and since that time, Papuans have taken up arms in an enduring resistance.

The decades-long push and pull of the Papua conflict deserves its own consideration, but for brevity’s sake, it can be understood at a surface level, as follows. Autonomous or semi-autonomous bands of Papuan rebels, loosely allied under the flag of the Free Papua Movement, have waged exclusively asymmetric war on Papua and the nearby islands. Operating in small groups, taking advantage of Papua’s treacherous landscape, those insurgents have mostly targeted the successive generations of Indonesian soldiers sent to impose order.

Indonesia’s counterinsurgent efforts have worked with the benefit of significant disparities in small arms, training and tactics, air and naval support, and intelligence, and Indonesia has used each of those assets to try and wipe out Papuan resistance wherever possible. For decades, those counterinsurgent efforts have included indiscriminate massacres of Papuan locals, including women and children. Torture, sexual violence, forced displacement, and imprecise naval and air bombardment have been routinely employed as weapons of war.

Nor are Papua’s rebels immune from allegations of indiscriminate violence. For many years, rebel bands have targeted not only soldiers, but teachers, medical personnel, infrastructure workers, and other outsiders who rebels alternately accuse of spying, or attempt to take hostage. Those attacks have only grown more common over time, as Indonesia has worked to develop Papua in order to assert its control, and facilitate the extraction of valuable resources.

In broad terms, the course of the conflict in Papua has been remarkably consistent across the decades. Although they may assert local control at the village level when Indonesian forces are not present, Papua’s rebels have never mustered the requisite force to take and hold significant territory. The conflict does rise and fall in intensity, however, and since 2018, the conflict has been quietly ramping upward.

In that year, Papuan rebels perpetrated the Nduga Massacre, the killings of nineteen construction workers and an Indonesian soldier. The massacre prompted a series of escalating crackdowns from the Indonesian government, and, in turn, those crackdowns prompted greater rebel action and the rise of a civil protest movement—which was then met with violent repressive action by Indonesia. By 2020, the United Nations was warning of “reports of extra-judicial killings, excessive use of force, arrest and continuous harassment and intimidation of protesters and human rights defenders”.

Across the 2020s, the fighting has only gotten worse. Bodies bearing signs of torture now appear regularly in conflict zones, while reports regularly allege extrajudicial executions carried out by Indonesian soldiers, including against children. Papuan rebels execute and mutilate civilians regularly, not just as retaliation for overtly collaborating with Jakarta, but in intermittent attacks on defenseless villages in Indonesia-controlled areas. Papuan civilians are under threat from all sides, and in a conflict without clear battle lines, people across the region face constant risk to their lives.

Screaming in Silence.

To the extent that the details of the Papua conflict are known at all, most available information is the result of dedicated work by local communities, to document and report the abuses perpetrated by all sides when it’s possible to do so. But perhaps more than any contemporary conflict on Earth, the war in Papua is defined by the sheer scale of its continuous information blackout. When reports do emerge from the conflict zone, they’ll often include hard details about a specific incident or confrontation, but they always come with the implication that far worse is happening, in the places nobody can see.

That information blackout is partially explained by the land on which the Papua conflict is fought, in one of the harshest, most unforgiving war zones anywhere on the planet. Much of its terrain is mountainous, thickly forested, or both, making it very difficult to navigate on foot, and all but impossible to navigate by any other means. It’s an incredibly biodiverse place, very humid and damp, and, in a practical sense, that means Papua is a place where bodies decompose quickly, helped along by an incredible volume of insects, arachnids, and small animals. When clashes take place in those areas, where no civilians or outside observers are around to keep records in real time, the evidence of a confrontation can disappear within just days.

Nor is it likely that an ordinary civilian, in those areas, would be able to report anything they’ve witnessed. Even today, much of Papua is underdeveloped; it lacks road infrastructure, internet access, and even dependable connections to a power grid. Information does not flow out of these areas, and nor does it flow in, except in cases where the presence of humanitarian groups or limited infrastructure projects can create some connection to the outside world.

In that environment, deadly chance encounters and secretive tactical chess matches between soldiers and rebels can, and probably do, go completely unchronicled. But even worse, both sides are at liberty to engage in egregious violence against each other, and against civilian populations. Most of the time, atrocities in these places will not be documented, and when they are, that documentation often won’t be shared for months or even years. Those who live in isolated zones, face severely elevated risk—and those who are captured or detained in other, more accessible places, can very easily be disappeared.

But even in combination, harsh terrain and a lack of development don’t explain the entirety of Indonesia’s information blackout. Instead, the worst of the blackout is deliberate, imposed and carefully cultivated by the Indonesian government.

In Indonesia’s domestic media environment, where censorship is typically fairly light, but can be overbearing on certain issues, reporting and discourse on the Papua conflict is sharply limited. Indonesian journalists and advocates face considerable restrictions on what they can report, and typically practice self-censorship as a result.

For those trying to report from inside Papua, the situation is far worse. Local reporters are frequently harassed by law enforcement and the military, as well as members of the Indonesian public who aren’t Papuan themselves. Violence against reporters and human rights advocates is relatively common, journalists are often paid off, and government agents are seeded into Indonesian news rooms, in an attempt to dictate and restrict coverage. In some cases, local journalists in Papua have been tortured or killed.

Foreigners, by contrast, don’t typically face violence…but that’s because they aren’t allowed in. Foreign journalists are subjected to very long, complex procedures to obtain a visa for Papua specifically, to the point that the process is prohibitively difficult and practically impossible, unless Indonesia trusts a foreign outlet to toe the line.

Against protesters, Indonesia has demonstrated a track record of consistent, disproportionate state intervention, no matter the issue, but protests that feature Papuan people or advocate Papuan causes, are among the most forcefully repressed. Peaceful demonstrations are frequently met with the use of excessive force, and demonstrators have had to scale back their action as a result.

Nor do rebel factions make it easy for outsiders to scrutinize the conflict zone. Foreigners are liable to be taken hostage for ransom, both because rebels know they can use the profits to boost their fortunes, and because they believe that kidnapping foreigners will result in increased media attention, as with the nineteen-month-long ordeal of Philip Mehrtens, a pilot from New Zealand who was taken captive in 2023.

In other cases, rebel groups can be distrustful of outside journalists, accusing them of being government-aligned infiltrators or even disguised members of the military, as they similarly accuse workers sent into the conflict zone. On occasion, rebel groups may be violent to those outside reporters, and in the fog of an ongoing conflict, violent misunderstandings can be hard to avoid—and can quickly turn fatal.

With so many disincentives to enter the conflict zone or to advocate for Papuans in Indonesia, and so little reason to believe that work can be done in a safe, effective way, journalists and advocates struggle to justify even attempting to investigate the conflict. In essence, this war has played out in near-silence.

In 2025 thus far, publicly available reports would suggest a death toll in the dozens. Any numbers that low, however, are likely to be an undercount by at least an order of magnitude.

Indonesia’s Endgame.

There’s a deeper question in all this: Why? Why does Indonesia insist so forcefully on prosecuting its war effort in Papua, to pacify and assimilate a remote, isolated corner of the country where, after more than half a century, this rebel movement still endures?

In part, Indonesia’s unwillingness to disengage is driven by the weight of history. On the one hand, Indonesia has pursued its claim to Papua, often quite violently, since the 1960s. The nation is home to a very large, very proud nationalist movement that its military and civil leaders have stoked for decades, and a claim on a place like Papua is not easily forgotten.

Not only that, but after decades spent in a cycle of violence, Indonesia would likely continue to come under attack from Papuan rebels, if it attempted to disengage from the conflict by offering anything less than Papuan sovereignty. The island’s rebels are invested just as deeply as Indonesia’s leadership, and there is no remaining trust between Indonesia and the people of Papua, to even consider a peaceful arrangement with Indonesia’s leadership.

Perhaps more important, at a moment in history where competition over resources is a growing global issue, Papua is home to immense mineral and biological wealth. It’s host to one of the world’s largest gold and copper mines, with significant deposits of oil, natural gas, and nickel, along with lucrative, salable timbers for harvest, and abundant offshore fishing waters.

Today, resource extraction from Papua makes up a growing share of Indonesia’s national revenues, and in response, Indonesia is working to expand its presence on the island, rather than drawing it down. Like other modern colonial powers trying to make inroads into contested territory, Indonesia has invested heavily in the development of new infrastructure, both to facilitate exploitation, and to allow for settlement by non-Papuan Indonesians.

At the center of that initiative lies the Trans-Papua Highway, a series of no fewer than twelve major roads—set to span a total of 4,325 kilometers—currently under construction across the island. The Free Papua Movement and other rebel representatives claim that the project mostly facilitates military expansion, and while it’s been successful in connecting previously isolated places to the outside world, those efforts have come with severe deforestation and a disregard for Papuan culture and well-being.

Well over 100,000 Papuans have been displaced by the project and other military-civil expansions over the last decade, and that number is only expected to rise further. According to many Indonesian experts and academics, however, the project is necessary despite the costs, to civilize a Papuan population that much of the Indonesian public regards as backwards or even savage.

That pessimistic outlook is only validated by Indonesia’s new leader, President Prabowo Subianto, who ascended to his post in October 2024. Although he’s popular among a share of Indonesians, Prabowo is a former military leader with a very extensive history of human rights abuses.

In 1983, he allegedly commanded the Indonesian forces that carried out the Kraras Massacre, in what was then the contested province of East Timor. Prabowo has also been accused of the kidnappings of at least twenty-two pro-democracy activists in Jakarta in the late 1990s, thirteen of whom are still missing today.

Since rising to the role of the presidency, Prabowo has faced growing allegations of authoritarianism, corruption, and manipulation of Indonesia’s government to serve his own ends. As a leader with deep ties to the Indonesian military, a record of alleged human rights abuses, and a vested past interest in facilitating counterinsurgent efforts, experts on Indonesia expected—even before he took office—that Prabowo’s tenure would see an escalation in the Papua region.

Today, those fears have largely been borne out. Indonesia is believed to have redoubled its troop deployments in Papua, dispatching thousands of additional soldiers to bolster counterinsurgent efforts. The use of drones to conduct precision strikes is reportedly on the rise, and the use of land mines, mortars, barrel bombs, and other explosives has grown increasingly standard. Activists even allege the use of white phosphorous.

The Indonesian military now regularly announces what it seems to view as successes, instances when a dozen or two dozen rebels might be killed, and some weapons or resistance symbols might be confiscated. Although Indonesia is less willing to acknowledge their operations’ darker side, Human Rights Watch reports that Indonesian troops have razed villages and attacked churches, while treating local hunters—armed with bows and arrows—as enemy combatants by default.

In some cases, Papuan advocates have insisted that the attacks that Indonesia publicizes, purportedly targeting separatists, have actually killed mostly civilians. In others, advocates report that government soldiers have realized that they can operate outside their mandate in the isolated jungles of Papua, and have started committing heinous acts of torture and mutilation against locals as they see fit.

Of course, those finer details don’t matter much to Indonesia, so long as accounts of what’s happening don’t ever leak out. Unfortunately for the people of Papua, it appears that it’s only a matter of time until projects like the Trans-Papua Highway are complete, and the saturation of Indonesian interests in Papua becomes too great to ever be undone.

The colonization of Papua is not yet complete, but barring a major reversal of Papuan fortunes, Indonesia seems to be on track to achieve the complete assimilation of the territory over the coming years and decades. The hidden carnage of the conflict zone is precisely that: Hidden, and neatly obscured from Indonesian and global public consciousness. Fail to change that, and there may be no way to prevent what’s happening in Papua, or to prevent Indonesia’s campaign from reaching its natural conclusion.

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