The outgoing president has presided over a growing tide of extremism
Mr. Yudhoyono has been neither a force, nor particularly moderate. Year after year, incidents of harassment and violence against religious minorities have increased to 264 in 2012 from 200 in 2009, according to democracy watchdog Setara Institute. The Communion of Churches in Indonesia says that at least 430 churches have been attacked, closed down or burned in the past decade. It's fairer to say that Mr. Yudhoyono has failed to stand up to extremists or protect minorities, and instead has exacerbated the problem.
Mr. Yudhoyono gave a speech in 2005 to the Indonesian Ulama Council (MUI), the highest body of Islamic clerics in the country, promising them "a central role in matters regarding the Islamic faith" and pledging openness to their fatwas "at any time." Interpreting this as a green light, within days the MUI issued a series of fatwas rejecting the religious pluralism on which Indonesia was founded and called for a ban on the Ahmadiyya, a Muslim sect regarded by conservatives as heretical.
Mr. Yudhoyono made another speech two years later implicitly endorsing the MUI's judgments. He promised that after a fatwa is issued, "the tools of the state can do their duty." In 2008, a government decree restricting Ahmadiyya activities was issued, and the persecution of the Ahmadiyya community has intensified.
Ahmadiyya were not the only target. A 2006 regulation on houses of worship led to the forcible closure of churches, and sometimes to violent attacks on them. Shariah-inspired regulations have spread across at least seven of Indonesia's 33 provinces and at least 51 out of 497 districts and municipalities. There are already at least 151 local Shariah regulations across Java, Sulawesi, Sumatra and West Nusa Tenggara. Most of these policies have been introduced by secular parties seeking political capital, rather than Islamists, but that doesn't make the rules any less potent in practice.
What is fueling this? In part, it is the government pandering to the minority Islamist agenda. Although Mr. Yudhoyono is not an Islamist, he has brought Islamists into his coalition for short-term political convenience. Another part is international consideration. Scholarships for Indonesian students, funding for Islamic boarding schools and literature come from Saudi Arabia and Yemen. As Australia's Lowy Institute notes, "the transmission of ideas runs largely in one direction: from the Middle East to Indonesia."
The scale of the challenge is now enormous. It is no longer just Christians and Ahmadis suffering, nor is the phenomenon confined to more conservative areas such as Aceh or West Java. It is now a nationwide problem affecting people of all religions. As shown by the case of Alexander Aan—released last month after two years in prison on blasphemy charges for declaring himself a nonbeliever—atheists are also vulnerable. So are mainstream Sunni Muslims who speak out in defense of religious freedom.
With elections coming up, there is an opportunity for Indonesia to change course. Indonesia has a tradition of religious pluralism and harmony which is rightly celebrated around the world. The country has much to be proud of, not least its transition from dictatorship to democracy. Were it to truly adopt a more moderate approach to religion's role in public life, it could be a model to others.
It is encouraging to know that there are Indonesians in government and civil society who are speaking up. One such voice is Syaiful Abdullah, a former leader of the Bandung branch of the notorious vigilante group the Islamic Defenders Front (FPI). He left the FPI after a change of heart, and now works to counter extremism. He urges international organizations to pressure the government, saying "The government has put its hands up, it does not know what to do anymore, so civil society needs to unite the inter-faith community to work together. My last hope is for the international community. Please do something. Make pressure, to guarantee protection."
As Mr. Yudhoyono leaves office, Indonesia's friends abroad, if they are true friends, should take these words to heart and do everything possible to urge the incoming government to undo the depressing legacy of the outgoing one. If not, Indonesia's pluralism will really be in peril.
Mr. Rogers works for Christian Solidarity Worldwide, an international human rights organization. He is author of "Indonesia: Pluralism in Peril–The Rise of Religious Intolerance Across the Archipelago," a report published Tuesday.