Islamic extremism and local governments have closed more than 100 churches in Indonesia within three years, according to a persecution watchdog agency.

From 2004 to 2007, 110 churches were closed in Indonesia as a result of attacks from radical Muslim groups or by local governments coerced by these groups, reports Compass Direct News.

Based on official numbers, a total of 1,025 churches have been closed or destroyed in Indonesia since the island nation claimed its independence in 1945. Notably, however, only two cases of church destruction or closures are recorded in the era of Indonesia's first president, Sukarno (1945 - 1967).

Provinces with the highest reported incidents of discrimination and violence against churches are West Java, Banten, Central Java, South Sulawesi and Bengkulu, according to the findings of the Communion of Churches of Indonesia, the Bishops' Conference of Indonesia, the Indonesian Human Rights Commission, and the Wahid Institute - a moderate Muslim non-governmental organisation.

In one recent incident, a church in Sepatan, Tangerang province, was attacked by extremists last December when it refused to adhere to government orders to shut down. Moreover, the home of the church's pastor was attacked by extremists who kicked out the home's windows and doors and threw out his possessions.

Indonesia is the world's most populous Muslim country with about 85 per cent of its 220 million people saying they are followers of Islam. Christians make up only about 8.7 per cent of the population, according to the CIA World Factbook.

The country has experienced much sectarian violence over the years with at least 1,000 people dying due to Muslim-Christian violence from 1998 to 2001 in Central Sulawesi province where there is roughly equal numbers of both communities.

High profile cases of Christian persecution in Indonesia include the 2005 arrests of three Christian Sunday school teachers who were accused of attempting to convert Muslim children.

The Muslim parents had reportedly given full consent for their children to join Christian students in singing Christian songs, playing games and hearing Bible stories, but the court nevertheless sentenced the women to three years in prison. The women served two years and were released early for good behaviour last June.

In 2005, Islamic militants on motorcycles beheaded three Christian schoolgirls as they walked to school. The girls' heads were dumped in villages nearby with a handwritten note placed next to the bodies warning of more killings in revenge for sectarian violence on Sulawesi Island.

"Wanted - 100 more heads," read the letter, according to The Associated Press. "Blood must be paid with blood, lives with lives, heads with heads."

While Muslims compose 86.1 of Indonesia's population, Protestants account for 5.7 per cent, Roman Catholics 3 per cent, Hindus 1.8 per cent, and others 3.4 percent, according the CIA World Factbook.