A US State Department report on religious freedom worldwide has highlighted the growing intolerance toward minority groups in Indonesia, amid a generally negative global trend that Washington calls worrying.

The "International Religious Freedom Report 2012," published on Monday, noted that the Indonesian government "generally respected religious freedom for the six officially recognized religions, but not for groups outside those six religions, or groups within those six religions that espoused interpretations that local or national leaders deemed deviant or blasphemous. "

"The trend in the government's respect for religious freedom did not change significantly during the year. However, as in previous years, the government sometimes failed to protect the rights of religious minority groups," the report said.

This included reports of police collaborating with hard-line groups against members of sects deemed to be "deviant," and the failure by security forces to act when radical non-state actors attacked minority sects.

There were also reports that government officials and police witnessed the coerced conversion of dozens of Shia followers to Sunni Islam in East Java, while local governments continued to block construction of houses of worship by minority groups within their communities. The national government failed to enforce two Supreme Court decisions in favor of construction permits for two Christian churches.

"There were reports of societal abuses and discrimination based on religious affiliation, belief, or practice. These abuses occasionally included incidents of majority-on-minority communal violence," the report said, adding that as a result of the violence, some 20 people were killed, hundreds of homes were destroyed and hundreds of people were displaced.

Several mentions were made in the report of the Islamic Defenders Front (FPI), a hard-line group that has agitated for the closure of Christian churches and mosques belonging to members of the Ahmadiyah and Shiite branches of Islam.

"Police appeared to act in concert with the FPI and other hard-line groups," the US report said.

"Through coordinated attacks, intimidation, coercion of – and sometimes in collaboration with – government actors, religious hard-line groups such as FPI, as well as local branches of the MUI [Indonesian Council of Ulema], often succeeded in restricting the rights of religious minorities."

It cited two events last May that the FPI managed to shut down or prevent, including a book discussion by Irshad Manji, a Canadian author known for her liberal interpretation of Islam, and a planned concert in Jakarta by the pop star Lady Gaga, which was called off after the FPI threatened violence if it was allowed on stage.

The decline in religious freedom in Indonesia was largely in keeping with the rest of the world, with the report highlighting a generally negative trend. "For 2012, some common themes regarding the status of religious freedom around the world emerged. In general, these themes reveal negative trends, and often cut across national and regional boundaries," it said.

The report comes three weeks after the US Commission on International Religious Freedom, an independent federal advisory body, issued its own report that warned that Indonesia's "rich tradition of religious tolerance and pluralism has been seriously threatened by arrests of individuals the government considers religiously deviant and violence perpetrated by extremist groups."