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n the latest damning assessment of religious freedom in Indonesia, the New York-based group Human Rights Watch (HRW) highlighted the government’s failure to protect religious minorities throughout 2012 in its global annual report.

The group’s World Report 2013 assessed progress on human rights during the past year in more than 90 countries, including Indonesia. In the 665-page report, the group said the Indonesian authorities took inadequate action against Islamist militants who mobilized mobs to attack religious minorities.

“Indonesia’s growing regional prominence is being held back by the government’s failure to confront intolerance of the country’s diverse political and religious views,” Phelim Kine, the deputy Asia director at HRW, said in a statement released on Thursday.

Citing the Setara Institute, a local NGO that monitors religious freedom, attacks against religious minorities rose from 144 cases in 2011 to 264 cases in 2012, the report said.

“Islamist militants mobilized mobs to attack religious minorities with impunity. Light prison terms imposed on those prosecuted sent a message of official tolerance for such mob violence. Dozens of regulations, including ministerial decrees on building houses of worship, continue to foster discrimination and intolerance,” the report said.

In a visit to The Jakarta Post on Thursday, HRW deputy program director Joseph Saunders, said the legislation was in place to protect religious minorities, including the Ahmadiyah and Shiite groups, but it was not being enforced.

“[President Susilo Bambang Yudhoyono] is not taking decisive action. He has weapons at his disposal that he is not using,” he said, citing the plight of the Christian congregations in Bogor and Bekasi in West Java that are still barred from attending their own churches, despite court rulings in their favor.

“Violence against religious minorities will only get worse as long as the Indonesian government encourages or ignores attacks by Islamist militants,” Kine said. “Indonesia’s leaders need to demonstrate real leadership and denounce the violence, revise discriminatory laws and ensure those responsible for abuses are punished.”

HRW hailed the credible and fair election in Jakarta and other provinces that it said underscored Indonesia’s ongoing transition from decades of authoritarian rule.

Indonesia, HRW said, had been seen as a role model for new democracies in the Arab world, but it was still beset by serious human rights problems.

The police, it said, were complicit in many acts of violence against minorities. It noted that on Aug. 26 last year, police officers stood by while hundreds of Sunni militants burned down 50 homes in a Shia village on Madura Island, killing one man.

“Indonesian authorities also failed to adequately protect artists, writers and media companies targeted by militant Islamist groups, who disrupted the May book tour of Muslim-Canadian writer Irshad Manji in Jakarta and Yogyakarta and caused the cancellation of a Lady Gaga concert in Jakarta in June,” the group said.

HRW also called on the government to release political activists in Papua who expressed their political views through peaceful means.

“The Indonesian government continued to prosecute peaceful political activists in Papua and the Moluccas Islands, conflating freedom of expression and association with armed separatism,” it said.

Presidential spokesman Julian Aldrin Pasha did not return calls for comment on Thursday.