By Murray Hiebert & Norashiqin Toh —

The election of Joko “Jokowi” Widodo in July 2014 marked Indonesia’s third direct and peaceful selection of the country’s president and seemed to consolidate the archipelago’s democratic gains. Given Indonesia’s impressive political transformation, the recent uptick in the harassment, intimidation, and violence toward minority groups has surprised many outside observers.

Findings published on February 23 by the Wahid Institute, an Indonesian advocacy group, reported 190 violations against freedom of religion and faith in 2015, a 23 percent increase from 2014. Targeted groups in the country that has the world’s largest Muslim country, most of whom follow the Sunni tradition, were often followers of the Shia sects, as well as Christians. In October 2015, a mob of Muslim hardliners attacked and burnt down several churches in Aceh Province, and several days later, the provincial government sanctioned the destruction of 10 more churches that had been built without permits.

Muslim hardliners have also targeted minority sects such as the Ahmadiyah and Gafatar religious communities. On January 24, the top elected official on Bangka Island off Sumatra said he would expel the Ahmadiyah community, and, five days later, district officials and Muslim clerics issued a notice banning Ahmadiyah activities in Subang district in West Java Province. More than 1,000 Gafatar members were evacuated on January 19 after a mob attacked their settlement in West Kalimantan Province and burnt it to the ground.

In December 2015, counterterrorism police foiled plots to attack Shia communities in Java and Sumatra, and in January the State Islamic University in Yogyakarta canceled a lecture by a Shia scholar after pressure from the hardline Islamic Peoples Forum (FUI).

Malioboro Street in Yogyakarta, a diverse city in Indonesia that was once a bulwark of tolerance. According to rights monitoring groups, the city now faces on average a reported case of intolerance each month.

Beyond growing intolerance toward minority religious groups, Indonesia has also witnessed an upswing in anti-lesbian, gay, bisexual, and transgender (LGBT) sentiments since January, which were sparked by Technology, Research, and Higher Education Minister Muhammad Nasir’s comment that the LGBT community should be barred from university campuses. The minister later said the LGBT community should be treated equally in the eyes of the law, but the uproar over LGBT issues continued.

Vice President Jusuf Kalla asked the United Nations Development Program not to carry out LGBT programs in Indonesia, and messaging app LINE was pressured into pulling its LGBT-related sticker sets. The Indonesian Broadcasting Commission issued a notice forbidding male actors from dressing or behaving effeminately on television, and the country’s largest Islamic organization, Nahdlatul Ulama (NU), called on both the Jokowi administration and the House of Representatives to begin preparing a law categorizing homosexuality as a crime.

High-profile officials have fanned much of this anti-LGBT rhetoric. Defense Minister Ryamizard Ryacudu on February 23 called the LGBT movement a form of proxy war more dangerous than nuclear war. Two days later, Tifatul Sembiring, a former communications and information minister, tweeted and then deleted a quote from the Prophet Muhammad implying that homosexuals should be killed. Hardline Islamist groups such as the Islamic Defenders Front (FPI) and FUI, continue to instigate verbal and physical attacks against minority communities and places of worship.

Much of this harassment and mob violence began under previous president Susilo Bambang Yudhoyono, who did little to rein in intolerant behavior during his term in office. Under his watch, persecutors of minorities were seldom brought to justice. Cabinet ministers signed a decree in 2008 ordering the Ahmadiyah community to “stop spreading interpretations and activities which deviate from the principal teachings of Islam.” In 2011, the then-religious affairs minister, Suryadharma Ali, repeatedly urged the cabinet to issue an outright ban on the Ahmadiyah and delivered a keynote speech at FPI’s congress in 2013 praising the hardline group as a “national asset” despite its harassment of religious minorities.

President Jokowi campaigned two years ago on a platform that prioritized respect for diversity in Indonesia, vowing to promote tolerance and restore the spirit of harmony among the country’s citizens. Although Jokowi spoke of the need to continue building positive interreligious communication and preserve tolerance in Indonesian society during the NU congress in August 2015, he has been noticeably silent since. Coordinating Minister for Political, Legal, and Security Affairs Luhut Pandjaitan has said Jokowi is still “listening to the people’s voice,” and the government is not in a hurry to address the intolerance issue. This failure to intervene, however, appears to have emboldened the voices of intolerance.

Sidney Jones, director of the Jakarta-based Institute for Policy Analysis of Conflict, cites several reasons for the increasing discrimination and threats against minorities in Indonesia.  One factor is the close ties between law enforcement agencies and hardline groups such as the FPI, which afford those harassing minorities significant impunity for their actions. Rather than protecting the victims, the police often stand aside during mob attacks and then blame victims for causing unrest. The government has also shut down places of worship under the guise of preserving public order, which has set a precedent for hardline Islamist groups to justify their actions.

Second, Jones says, is a significant anti-foreigner sentiment among conservative nationalists such as Defense Minister Ryamizard who “promote the idea that Indonesia is besieged by enemies trying to destroy Indonesia from within [by] imposing their values” through such activities as supporting the LGBT community. A third cause is “the concerted push by many Islamist organizations for the government to play a greater role in setting standards for both morality and religious orthodoxy,” Jones argues.

Finally, Jokowi’s continued silence has allowed many officials in his government to speak out. Without the pressure to stick to a united voice, Jones says many are simply looking for issues to put themselves in the spotlight. The result is an assault on the civil liberties of minority groups in Indonesia.

The increasing rhetoric and moves against religious and sexual minorities could have longer-term implications for Southeast Asia’s largest economy. They could add to the existing perception that Indonesia does not welcome foreign investors, and deter companies—especially those in the digital space—from setting up operations in Indonesia, or tourists from coming in the future.

To be sure, the mounting intolerance is an issue that Indonesians must work out on their own, but governments such as that of the United States — while admitting with humility their own problems on this front — can play a useful role by shining a spotlight on cases of prejudice and reminding Jokowi’s government of the president’s campaign promise to promote “unity in diversity.”

Mr. Murray Hiebert is a senior adviser and deputy director of the Southeast Asia Program at CSIS. Follow him on twitter @MurrayHiebert1. Ms. Norashiqin Toh is a researcher with the Southeast Asia Program.