Indonesia’s Papua Sees Deadly Fighting With Christians In Crossfire (Worthy News Investigation)

by Stefan J. Bos, Worthy News Chief International Correspondent

JAKARTA (Worthy News) – Concerns are mounting about the future of Indonesia’s predominantly Christian Papua region, where the army claims to have recaptured a village in deadly clashes with separatist rebels amid reports of civilian suffering and long-standing grievances over Jakarta’s rule.

The Indonesian military said it had retaken Soanggama village on October 15, 2025, in Central Papua’s Intan Jaya district after what it described as a six-and-a-half-hour battle with the West Papua National Liberation Army, the armed wing of the separatist Free Papua Organization.

Lieutenant Colonel Iwan Dwi Prihartono, a military spokesman, said 14 insurgents were killed and that no government troops died in the operation. He added that soldiers seized a homemade rifle, four air rifles, ammunition, communication gear, documents, and a separatist “Morning Star” flag.

However, rebel spokesman Sebby Sambom disputed that account, claiming that only three of the dead were fighters and that nine civilians were killed when troops allegedly surrounded a home believed to shelter rebels.

Independent verification of either side’s claims remains nearly impossible due to restricted access and the region’s remoteness.

CHURCHES UNDER FIRE

The confrontation follows a pattern of attacks and reprisals that have increasingly endangered Christian communities and missionaries in the conflict-torn highlands.

In March 2025, armed separatists attacked a Catholic-run school in Yahukimo Regency, killing 30-year-old teacher Rosalia Rerek Sogen and injuring several others, according to local church officials and Indonesian media.

In May 2025, shelling near a church in Puncak Regency killed an 18-year-old student, explained human rights monitors.

Church leaders and rights groups have warned that security forces have used church compounds and mission buildings as temporary barracks or lookout posts, blurring the line between civilian and military sites and placing congregations at risk of rebel retaliation.

Amid the ongoing violence, Mission Aviation Fellowship (MAF) — an American Christian humanitarian aviation group — continues to serve isolated valleys with flights carrying aid and missionaries. Its pilots face persistent danger: on May 12, 2020, an MAF Quest Kodiak aircraft crashed into Lake Sentani shortly after takeoff from Papua’s Sentani Airport, killing its American pilot, Joyce Lin, who was delivering COVID-19 relief supplies.

LONG-RUNNING GRIEVANCES

Rebels in Papua have waged a low-level insurgency since the 1960s, when Indonesia assumed control of the former Dutch colony, which now comprises six provinces with a combined population of roughly 5.5 to 6 million people, according to the Central Statistics Agency (BPS).

The territory’s 1969 U.N.-sponsored referendum, known as the “Act of Free Choice,” involved about 1,026 hand-picked tribal representatives voting under military supervision and is widely viewed by historians and human rights groups as lacking legitimacy.

Despite its mainly Christian identity, Jakarta insists that Papua’s integration into Indonesia — the world’s largest Muslim-majority nation — is final. Officials say government programs have expanded infrastructure, healthcare, and education in previously neglected areas.

Yet indigenous Papuans, mostly Christian Melanesians, say they remain marginalized and subjected to harassment by security forces guarding lucrative mining, gas, and logging projects run by Indonesian and foreign companies.

Papua holds some of the world’s richest gold and copper deposits, including the Grasberg mine, one of the largest globally and a key pillar of Indonesia’s export economy.

ENDURING DISPLACEMENT

Critics told Worthy News that profits from Papua’s vast natural resources rarely reach local communities, who instead endure displacement, environmental damage, and intensified military operations aimed at securing resource zones.

Human rights monitors estimate that tens of thousands of Papuans have been displaced by fighting in the highlands over the past two years, amid reports of burned homes, destroyed churches, and blocked aid routes.

The Papuan Council of Churches and several international observers have called for renewed dialogue and independent investigations into alleged human rights abuses. The council has urged Jakarta to halt military operations near schools and churches and to allow humanitarian access to conflict zones.

As gunfire and helicopter patrols continue across Papua’s mist-covered mountains, many fear that Indonesia’s longest-running separatist conflict is again escalating — and that the region’s Christian heartland will continue to bear the heaviest burden.

(Worthy News sources in Indonesia contributed to this story.)

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