Indonesia’s Christian Legacy and the Silent Islamization of Papua

A historical photograph captures a symbolic moment:

Soekarno, Indonesia's first president, standing alongside Msgr Georges de Jonghe d'Ardoye, the Vatican’s first apostolic delegate to Indonesia, and Msgr Albertus Soegijapranata, the first native Indonesian bishop.

The image reflects a forgotten truth — the founding of the Indonesian republic was not merely the result of nationalist or Islamic struggle, but also deeply indebted to Christian contributions.

Christians and the Birth of the Nation

Throughout Indonesia’s early years, many Christians were central to its political, educational, and diplomatic development. From Dr. Johannes Leimena, vice prime minister under Sukarno, to Bishop Soegijapranata’s famed declaration “100% Catholic, 100% Indonesian,” Christians affirmed their commitment to the new republic.

The Catholic Church supported Pancasila, the pluralist state ideology, and helped shape a nation where every religious community could coexist under mutual respect. Yet, over time, the promise of that vision has eroded.

State Privileges for Islam

Indonesia proclaims itself a religiously neutral state, but government policy tells a different story. Islam enjoys institutional support unlike any other faith:

The Ministry of Religious Affairs dedicates the majority of its budget (over 60%) to Islamic programs, more than twice the budget of the Ministry of Transportation (Tempo, 2023).

There are state-funded Islamic universities (UIN), Islamic courts, zakat (alms) laws, halal product regulations, and state-sponsored Hajj pilgrimages — all absent for Christian or other religious traditions.

Public funding for Islamic development dwarfs allocations for other faiths, fostering structural inequality.

The Pontifical Council for Justice and Peace, in its Compendium of the Social Doctrine of the Church, warns against such favoritism:

“The religious freedom that must be guaranteed to all cannot become the basis for privileging one religion over another” (§423).

Yet this is precisely what is happening in Indonesia.

The Hidden Islamization of Papua

Nowhere is this injustice more visible than in West Papua, a territory with a Christian majority forcibly annexed into Indonesia through the controversial New York Agreement (1962) and the sham "Act of Free Choice" (1969) — a process the UN itself described as conducted under duress.

At the time of annexation, Jayapura, the provincial capital, had only one mosque. Today, there are over 260. State-sponsored transmigration programs, combined with selective religious infrastructure investment, have accelerated the demographic and religious transformation of Papua.

Even more concerning is the spread of mosques inside military and police compounds, symbols not only of Islam but also of state power. The 2008 Anti-Pornography Law, inspired by Islamic conservative groups, has further entrenched Sharia-style policies at the local level, despite protests from non-Muslim communities.

The Church teaches that religious freedom includes freedom from coercion, including cultural and demographic pressures that undermine a community’s identity (Dignitatis Humanae, §2–4). The forced Islamization of a historically Christian region under a secular constitution is a clear violation of this principle.

Double Standards and Church Attacks

The construction of churches is notoriously difficult due to bureaucratic restrictions under Joint Ministerial Regulation No. 8/9 of 2006, requiring the approval of at least 60 local residents and the support of local authorities — hurdles that are easily exploited to block Christian churches.

Since Indonesia's independence, over 2,400 churches have been attacked, destroyed, or shut down. Despite this, there has been no consistent legal action against the perpetrators. Contrast this with the swift punishment when Islamic symbols are threatened.

As Pope Francis stated in Fratelli Tutti (2020):

“Religious freedom must never be used as a pretext for imposing a particular religion or cultural model on a minority” (§285).

But in Papua, religious freedom exists mostly on paper.

Will Papua Still Be Christian in 2055?

In 2055, Papua will commemorate 200 years since the arrival of Protestant missionaries Ottow and Geissler, who first brought the Gospel to the region. Yet many fear that by then, Christian Papua will be little more than a memory.

The demographic shift, combined with religious marginalization and political repression, is pushing indigenous Papuans to the margins of their own land. The churches they built, and the faith they embraced, are increasingly overshadowed by a state apparatus aligned with one religion.

A Call to Conscience

The Catholic Church teaches that truth and justice are non-negotiable in public life (Evangelii Gaudium, §183–184). And yet, as long as the Vatican remains diplomatically silent about the systematic religious favoritism in Indonesia — particularly in its eastern provinces — it risks betraying those very principles.

In Gaudium et Spes, the Second Vatican Council proclaimed:

“The joys and the hopes, the griefs and the anxieties of the people of this age… especially of those who are poor or in any way afflicted, these are the joys and hopes, the griefs and anxieties of the followers of Christ” (§1).

The people of Papua are afflicted. Their land, culture, and faith are under siege. It is time for the global Church — and especially the Vatican — to speak clearly and courageously.

Because silence is not neutrality. It is surrender.