Human Rights Watch is calling upon the Indonesian President to intervene to put a stop to the demolition of churches.
The call was made by Human Rights Watch following reports that a local government demolished a new structure of the Batak Protestant Christian Church (HKBP) in Bekasi, a suburb of Jakarta, on 21 March.
The demolition was reportedly ordered at the behest of the Islamic People's Forum in Taman Sari, a militant Islamist organisation, because the church did not have a building permit.
Videos of the demolition on YouTube show church members crying and begging officials not to demolish the church. As the building comes down, Muslim militants cheer and shout out Koranic verses.
"The government's demolition of a church in Bekasi not only violates religious freedom, but it will fan the flames of religious division in Indonesia," said Brad Adams, Asia director at Human Rights Watch.
"President Yudhoyono needs to reverse the decision, compensate the congregation, and publicly order an end to the destruction of houses of worship."
He continued: "Demolishing a religious minority's house of worship because of opposition from the majority creates a dangerous precedent.
"The government may be unleashing forces that it will not be able to control."
Human Rights Watch said it was becoming increasingly difficult for Christian churches in traditionally Muslim-majority areas to obtain building permits.
West Java, where Bekasi is situated, is one such area where there has been an increase in the Christian population.
In some cases, it has taken churches over 10 years to receive the necessary approval. The demanding requirements include the names and ID cards of at least 90 congregants, a support letter from at least 60 other local residents, and written recommendations from the Religious Affairs Ministry and the Religious Harmony Forum, a consultative body of local religious leaders.
More than 20 HKBP churches are operating without a building permit, leaving them exposed to the threat of demolition.
HKBP Filadelfia has been refused a building permit by the local government despite the Indonesian Supreme Court approving construction.
Human Rights Watch said the government must revoke discriminatory regulations requiring houses of worship to be built with the approval of a regional administrator.
Although the regulations apply to all religions, Human Rights Watch said they were being used in practice to discriminate against religious minorities.
There are reports of Muslim militants using the strict regulations as justification for vandalising and torching so-called "illegal" churches.
Between 2010 and 2012, there were at least 30 documented church closures in Java and Sumatra, and one mosque closed in Kupang.
Cases of violence against Christians, Ahmadiyah and other religious minorities have increased since President Susilo Bambang Yudhoyono came to power in 2004.
According to figures from the Communion of Churches in Indonesia, more than 430 churches have been attacked, closed down, or burned down since 2004.
Adams called for action to halt the violence against religious minorities.
"The government needs to recommit itself to religious freedom for all communities," he said.
"By providing principled leadership it can calm the situation down. But if it gives in to extremists, there will only be more social divisions and violence in the future."