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Outgoing President Susilo Bambang Yudhoyono broke his long silence on violent religious extremism the other day, describing it in an Aug. 21 interview as “shocking” and “becoming out of control.”

To the dismay of the many Indonesians who have fallen victim to the country’s rising tide of religious intolerance, Yudhoyono’s concerns were not for plight of the country’s besieged religious minorities, but rather a response to the actions of the Islamic State in Iraq and Syria. That group’s well-documented brutality and indications that Indonesians are joining its ranks is certainly cause for worry.

But Yudhoyono’s comments betray a troubling lack of concern about the acts of harassment, intimidation and violence suffered by Indonesia’s own religious minorities from Islamist militants during his decade as president. Instead, Yudhoyono downplayed such incidents in Indonesia by claiming it is “understandable that sometimes there will be conflict between different groups.”

That is more than gross understatement. Indeed, it could summarize the Yudhoyono government’s sorry record in adequately confronting religious intolerance and related violence during his administration. During the last decade, there have been numerous incidents of harassment, threats and violence against religious minorities. Indonesia’s Setara Institute, which monitors religious freedom in Indonesia, documented 220 cases of violent attacks on religious minorities in 2013, an increase from 91 such cases in 2007.

The targets? The many Christian congregations, Shiites and the Ahmadiyah. These groups have become targets of Sunni militant groups who label most non-Muslims as “infidels,” and Muslims who do not adhere to Sunni orthodoxy as “blasphemers.” Even Indonesia’s atheists live in fear of such groups.

The increasing violence against religious minorities — and the government’s failure to take decisive steps against it — does more than put the lie to Yudhoyono’s sunny assessment of Indonesia as a country in which “We respect all religions.” The government’s inaction violates guarantees of religious freedom in the Indonesian constitution and Indonesia’s obligations under the International Covenant on Civil and Political Rights, which Indonesia ratified in 2005.

Indonesia’s Shiite minority has had particular reason to worry in recent weeks. In April, the Anti-Shiite Alliance, a gathering of militant Sunni organizations, attracted thousands to hear speeches advocating “jihad” against the country’s Shiite minority. Among the participants were members of one of the country’s most violent Islamist organizations, the Islamic Defenders Front (FPI). The FPI that day opted for a uniform of black ski masks and camouflage jackets stenciled with the term “Heresy Hunters” to leave no question about their intentions.

But while Yudhoyono frets publicly about the far-away threat of the Islamic State, he and his government have allowed the FPI and kindred groups to carry out violence against religious minorities with near impunity. A June 2008 FPI attack on representatives of the interfaith National Alliance for Freedom of Faith and Religion at the base of the National Monument (Monas) in Jakarta injured dozens. More recently, the FPI forced the closure of an Ahmadiyah mosque in West Java in October 2013 after threatening to burn it down. Rather than confront the FPI, Yudhoyono and his government have chosen to coddle it. On Aug. 22, 2013, Indonesia’s then-religious affairs minister, Suryadharma Ali, opted to make the keynote speech at the FPI’s annual congress in Jakarta at which he praised the group as a “national asset.”

But Yudhoyno’s failure to protect religious freedom goes far beyond his acceptance of the depredations of Islamist thugs. On multiple occasions in recent years, police and government officials have been passively or actively complicit in incidents of harassment, intimidation or violence against religious minorities.

On Feb. 6, 2011, police stood by while a group of some 1,500 Islamist militants attacked 21 members of Cikeusik’s Ahmadiyah community who were holding a prayer meeting in a private home. The militants bludgeoned to death three Ahmadiyah men and seriously injured five others. A court sentenced 12 of the perpetrators to token prison sentences of three to six months. Adding insult to injury, the court also sentenced an Ahmadiyah man to a six-month prison term for merely attempting to defend himself. Police have yet to publicly release the results of their internal investigation into the attack.

Moreover, Indonesian government officials and security forces have often facilitated harassment and intimidation of religious minorities by militant Islamist groups. That includes making explicitly discriminatory statements, refusing to issue building permits for religious minorities’ houses of worship, and pressuring congregations to relocate. Such actions are in part made possible by discriminatory laws and regulations, including a blasphemy law that officially recognizes only six religions, and house of worship decrees that give local majority populations significant leverage over religious minority communities.

Indonesian government institutions have also played a role in the violation of the rights and freedoms of the country’s religious minorities. They include the Ministry of Religious Affairs and the Coordinating Board for Monitoring Mystical Beliefs in Society (Bakor Pakem) under the Attorney General’s Office. Also, the semi-official Indonesian Ulema Council (MUI) has eroded religious freedom by issuing decrees and fatwas (religious rulings) against members of religious minorities and pressing for the prosecution of “blasphemers.”

Yudhoyono will step down as Indonesia’s president in late October, leaving a toxic legacy of rising religious intolerance and related violence.

A key challenge of his successor, Joko Widodo, or Jokowi, will be to take immediate steps to recognize and reverse the malign impact of Yudhoyono’s decade of failure in protecting religious freedom. Prioritizing protection for the country’s religious minorities and a zero-tolerance policy for abuses by Islamist militants will be a vital step toward that goal.

Phelim Kine is a former Jakarta-based foreign correspondent and the deputy director of the Asia division at Human Rights Watch

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