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On December 1, 1961, the Dutch flag that had flown over the peninsula of West Papua for more than 130 years was replaced by the “Morning Star” flag.  This signified an important transition for West Papua – away from colonialism, to a new start as a free nation.

By the end of the decade, Indonesia had forcefully annexed West Papua (also known as West Irian at the time) with tacit support from the United States. But 50 years later – an anniversary that was marked this week – National Flag Day was remembered by the West Papua independence movement. Resistance leaders and human rights advocates recalled the brutal military takeover of the country by Suharto’s Indonesia, as well as the hope that the “Morning Star” flag still epitomizes today.

Indonesia was granted independence from the Netherlands in 1949, but the Dutch maintained control over West New Guinea. U.S.-sponsored mediation between the former colonizer and colonized led to Indonesia assuming full control of the region by the end of 1962 on the condition that Jakarta would allow a local vote on the issue of self-determination under United Nations supervision.

What followed was a decade-long crackdown on any manifestations of political opposition and dissent by Suharto. The “Act of Free Choice,” held under dubious conditions in 1969 and under which Jakarta handpicked elders of the Papuan community to agree to become part of Indonesia, was supported and recognized by the West and the United Nations.  The “community elders” have been widely quoted since then as saying that they were forced to vote at gunpoint to be part of Indonesia.

Indonesia’s crimes in Timor-Leste during the Cold War era until the end of the 20th century are well documented. But Indonesia’s behavior in West Papua over the past half century has been underreported in mainstream news outlets. During this period, approximately 100,000 Papuans were killed – almost 10 percent of the population. The Yale Law School has labeled it genocide. Evidence of Indonesia’s repression is revealed in the exploitation of West Papua’s land and resources, as well as scores of accounts of rape, torture, and extrajudicial killings.

The separatist Free Papua Movement (OPM) was set up in the mid-1960s in response, and began waging a guerrilla struggle against the Indonesian military. The erosion of Papuan culture and tradition was the raison d’etre for leaders of the movement, and an armed struggle has persisted on and off in the decades since.

In the 1980s, Jakarta launched Operation Clean Sweep, which targeted family members of OPM fighters in an effort to defeat the movement. Electric shocks, public rapes, and death by bayonet were just some of the methods employed by Indonesian soldiers.

In Jakarta’s attempt to exploit the region’s wealth of gold, copper and timber, West Papuan villagers were routinely uprooted from their homes without any compensation, and without the required labor skills to survive such a transition. Forced labor of many indigenous tribes in West Papua was also common practice; resistance was typically met with torture.

West Papua has also long been a victim of socioeconomic neglect: access to education is minimal, 42 percent of the population lives below the poverty line, and the prevalence of HIV/AIDS has exploded.

Today, it’s a crime to fly the “Morning Star” flag, as the world found out through the infamous incarceration of activist Yusak Pakage, a prisoner of conscience according to leading human rights groups.

West Papua was given special autonomy status in 2001, but human rights abuses, committed by Indonesian paramilitary forces, persist to this day. The West has gradually begun to apply additional pressure on Jakarta to ease its treatment of civilians in West Papua, but it hasn’t nearly matched the effort that observers have seen exerted on governments in other, well-publicized areas of the world.

Indonesia needs the West as much as the West needs Indonesia. It’s a complex area of U.S. foreign policy, but the success of such symbiotic relationships is predicated on transparent dialogue and communication between the two parties. The 50th anniversary of National Flag Day should be used by Washington and other Western governments as a way of highlighting the situation of West Papuans so as to bring some justice to this continued struggle, as well as attempt to modify Jakarta’s Papuan policy even further.