Indonesians also could encourage Islam to move in a more tolerant direction. The population is 88 percent Muslim, 9 percent Christian, 2 percent Hindu, and 1 percent Buddhist. Despite the size of its Muslim population, Indonesia’s politics traditionally have been secular. The Islam practiced by most of its adherents is moderate. In its new report, “In Religion’s Name: Abuses against Religious Minorities in Indonesia,” Human Rights Watch (HRW) noted that “Indonesia is rightly touted for its religious diversity and tolerance.”

Yet like Iraq, Tunisia, and Egypt, the end of dictatorship in Indonesia has loosed intolerant religious forces. Observed HRW, increased freedom has encouraged a number of “long repressed” viewpoints, including “religious militancy.” The success of Islamic radicals, in particular, “stands in stark contrast to the Indonesian government’s claims of adherence to the country’s constitutional guarantee of religious freedom,” noted Phelim Kine, deputy director of HRW’s Asia division.

The victims are many. Reported HRW: “Targets have included Ahmadis (the Ahmadihay), Baha’is, Christians, and Shias, among others.” Offenses range from state discrimination to social bullying to mob violence. Although religious minorities have not been without blame in areas where they dominate, “In most cases, the perpetrators of the intimidation and violence have been Sunni militant groups… at times acting with the tacit, or occasionally open, support of government officials and police.”

As the most populous religious minority, Christians are most often the targets of intolerance and violence. Indeed, warned the group International Christian Concern, “anti-Christian hostility is only escalating in a country which lacks the political will to enforce the values of its constitution.” Explained ICC, the shift of power from Jakarta after Suharto’s fall “empowered local leaders to let conflicts simmer and delay, if not entirely dismiss the rule of law, so that Christians fall prey to all manner of religious oppression, ranging from denial of building permits to bombings, threats, killings and forced conversions.”

One problem area, explained HRW, is that religious minorities “have difficulties obtaining permits to build places of worship and, in the worst cases, become targets of violence.” From 2005 and 2010, for instance, 430 churches were forcibly closed.

HRW found “at least 12 cases in which militant groups have used [the regulations issued in 2006] to block the establishment of new houses of worship and to close 31 existing houses of worship.” Moreover, “Even in cases where a permit is issued for a house of worship, vociferous responses from militant groups have caused local officials to rescind them or the groups prevent the applicants from constructing or using the building. The Indonesian government and local authorities routinely fail to take measures against the Islamist groups.” Local officials, whether out of conviction or fear, sometimes take up the radicals’ “call to encourage minority congregations to move to different areas.”

The report detailed “sustained campaigns against two high-profile Christian churches, that of the GKI Yasmin church in Bogor, and the HKBP Filadelfia church in Bekasi, West Java. Both of these churches had not only secured all administrative documents and political approvals, but won Supreme Court challenges to secure their building permits. Despite these favorable court decisions, local government authorities denied building permits to the two churches.” Then Jakarta failed to enforce the judicial rulings.

Sunni fundamentalists also have targeted Hindus and even Shia communities. HRW found one case when Christians in a predominantly Christian area used similar tactics to build a mosque, and the group suspects that there are other instances. Although religious liberty should be respected in all cases, the position of Rev. Judith Nunuhitu-Folabessy reflects a certain logic: “Our Christian brothers and sisters in Java have to obey the 2006 regulation. We want that regulation to be implemented here as well. If we don’t want to follow that regulation to the letter, then it should not be implemented that way in other parts of Indonesia.”

Moreover, HRW pointed to the use of blasphemy and conversion laws “to impose criminal penalties on members of religious minorities in violation of their rights to freedom of religion and expression.” Such abuses are common in Pakistan, where violent jihadist sentiments are strong. All religious minorities, as well as atheists, are at risk.

Expansive state control gives government many other avenues for discrimination if not persecution. HRW reported: “state discrimination on the basis of religion extends beyond the building of churches, mosques, and temples. Various government regulations discriminate against religious minorities, ranging from the provision of ID cards, birth and marriage certificates, and access to other government services.”

For instance, officials refuse to register marriages if the government doesn’t recognize the religion of one of the parties. Without registration children are not issued birth certificates listing both parents. National ID cards are required, but sometimes cannot be obtained without choosing among five officially recognized religions. Refusing to list a religion can lead to charges of atheism and blasphemy.

Many of the problems faced by religious minorities result from flawed laws. Reported HRW: “The harassment and violence directed at minority religious groups is facilitated by a legal architecture in Indonesia that purports to maintain ‘religious harmony,’ but in practice undermines religious freedom.”

Indonesia’s constitution recognizes religious liberty and Jakarta has signed international agreements affirming this fundamental right. However, even the United Nations, hardly a hotbed of freedom of conscience, cited Indonesia’s “tendency to discriminate against any religion or belief for any reason” and laws which “can violate freedom of religion or belief.” The ever-diplomatic State Department in its latest report on religious liberty in Indonesia acknowledged that “some laws and regulations restrict religious freedom.”

The HRW report cited several measures which undermine religious liberty. One is a constitutional amendment from 2000 which requires citizens “to accept the limitations determined by law” in order to promote other social ends. Explained HRW: “The latter provision has been and continues to be invoked to demand that religious minorities cater to the demands of the religious majority. By 2010, Indonesia had at least 156 statutes, regulations, decrees, and by-laws that restrict religious freedom, many of them justified by reference to” this constitutional article.

The 1965 blasphemy statute, enacted under Suharto’s predecessor, was approved under “Pressure from Muslim conservatives.” In contrast to Pakistan, at least, the punishment prescribed is prison rather than death. Two government ministers defended the law in court; reported HRW, “They said Muslim mobs would probably attack religious minorities if the blasphemy law were overturned, believing it their duty to defend their religion if Islam is being tarnished.”

Two decrees regarding the construction of houses of worship restrict “the construction of houses of worship.” The measures require the approval of local authorities and support of local communities. No surprise, noted HRW, “These regulation have especially been used to discriminate against Christians who seek to build churches.”

Laws and decrees covering proselytizing, child protection, and the Ahmadiyah also have been used to directly interfere with religious liberty. These measures are backed by “various governmental and quasi-governmental institutions [which] have played a key role in promoting a Sunni Islamic identity in Indonesia at the expense of minority religions.” Although the Ministry of Religious Affairs nominally addresses all faiths, its current head, Suryadharma Ali, explained HRW, “has been outspoken against religious minorities.” Despite his image as a modernizer, President Susilo Bambang Yudhoyono has allied himself with some of Indonesia’s most retrograde elements.

Misuse of legal rules and processes to hinder religious practice is bad enough. Worse is the government’s failure to protect religious minorities from violence. Such attacks, while not exactly common, are not unusual either, and are becoming more frequent. The Indonesian human rights group, the Setara Institute for Democracy and Peace, reported 264 violent attacks in 2012, up from 244 and 216 incidents, respectively, in 2011 and 2010.

Over the years I visited a church and Bible school destroyed by mobs, as well as a church which was bombed — costing the pastor’s wife a leg. In none of these cases were the culprits apprehended, let alone punished.

The violence continues. ICC pointed to an attack in January by Islamic radicals on the minister of a Protestant church in West Java while he was leading a worship service. None of the thugs were arrested, but two days later the pastor was charged for acting without a building permit. Earlier this year Setara’s deputy chairman Bonar Tigor Naipospos observed that “Cases of intolerance against Christians remained high in the country.”

Although Christians are targeted for violence most often, they are not alone. The State Department reported on Ahmadiyas displaced by mob violence in 2006 who remained displaced, essentially refugees in their own country. HRW cited a 2011 attack on a Shia boarding school in which “more than 200 Sunni militants entered [the facility] and destroyed school property. In the course of defending themselves, nine teenage students were injured.”

The authorities rarely do act. HRW reported on “incidents in which police failed to take action to prevent violence against religious minorities or provided no assistance in the aftermath of such incidents. Police all too often have been unwilling to properly investigate reports of violence against religious minorities, suggesting complicity with the perpetrators. Nor has the justice system proven to be a defender of religious minorities. In the few cases of violence that have gone to the courts, prosecutors have sought ridiculously lenient sentences for the perpetrators of serious crimes, which the judges seem content to oblige.”

In this way the Indonesian government is not fulfilling its most basic responsibility. Even State reported that “Due to inaction the government sometimes failed to prevent violence, abuse, and discrimination against individuals based on their religious belief.”

The examples are many, well documented by HRW. Explained the organization: “In some instances, police actively collude with the attackers for religious, economic, or political reasons; in other instances, they lack clear instructions from above or feel outnumbered by militants. In all cases, the poor police response reflects institutional failure to uphold the law and hold perpetrators of violent crimes to account.” Prosecutorial and judicial failures reinforce the refusal to protect the most vulnerable in Indonesia.

And the problem is not just occasional and episodic. Noted HRW: “In some areas of Indonesia, the intimidation and threats against religious communities by Islamist groups have persisted over time, with little effort from government officials to curtail the violations. Of particular note is the continued coddling of the Islamic Defenders Front (Front Pembela Islam, FPI), which has engaged repeatedly in acts of violent vigilantism.” Government and police officials even have appeared at FPI events and called the organization a partner in preserving law and order. The International Crisis Group noted that “Taking on allies known for their intolerance is not the way to inculcate religious harmony.”

Not that the Indonesian government appears to be concerned. Bahrul Hayal, Indonesia’s Secretary General of Religious Affairs, acknowledged “one or two cases” of violence, “but I want to say that the achievements [in responding] are better and getting better and I expect that the maturity of the people will also improve over time.”

One can only hope. Last year the State Department warned of “some deterioration in the protection of the right to religious freedom” in Indonesia. Moreover, noted HRW, Jakarta’s failure to respond decisively when “intolerance is expressed through acts of harassment, intimidation, and violence” is “creating a climate in which more such attacks can be expected.”