A 2006 housing ruling - the Joint Ministerial Decree on Religious Building Permits - states that religious groups must get approval from their local community, by way of signatures, to build a 'house of worship'.
It says there must be 60 signatures from households of a different faith and a list of 90 potential members, as well approval from higher district authorities.
However, Christians say they cannot get enough signatures from Muslims in their communities, who make up 79 per cent of the nation, and that churches are therefore not getting built.
According to religious freedom charity Open Doors, a Baptist church on the island of Java had building work stopped in August because their building permit - granted in 1998 - had expired.
Government offices also broke up a church service in August in Riau, on the island of Sumatra where a Pentecostal congregation was worshipping in the yard of their church because the building had been sealed off by the authorities citing the lack of a building permit.
The church's pastor, Ganda Damianus Sinaga, has applied for a permit but is finding it difficult to get one issued.
A Pentecostal church in Yogyakarta, also on Java, had applied for and obtained a permit but local authorities revoked it because the church failed to meet the requirement of using its building 'frequently'.
Before the decision, threats had been made to church members from local hard-line Muslim groups not wanting the church in their community.
An Open Doors spokesperson said: "Failure to obtain a building permit has been widely used as an excuse by the Islamic religious authorities to justify closing churches in Indonesia. For minorities, like Christians, it is hard to gather enough signatures from the majority Muslims. And, even if they succeed, approval from the government may take years, even decades.
"But the real challenge for President Jokowi's government, which has started its second term, is the increase in conservative and radical Islam among the population.
"Reports on the changing attitudes of Indonesian citizens are pointing to the fact that the Islamic population is becoming religiously more conservative and that 'religious harmony' is valued higher by many Indonesians than 'religious freedom'.
"Although the idea of 'religious harmony' might seem appealing, it is dangerous if it means that the majority religion has the right to not be disturbed by minority religions."
Indonesia is currently number 30 on the Open Doors World Watch List, a ranking of 50 countries where it is most difficult to live as a Christian.
Christians do not normally face violence there but there is increasing pressure on Christian from Muslim backgrounds and some regions operate under Islamic law.
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