Church leaders were told they could only continue to hold them if they obtained permission from the district official's collector's office.
However, Pastor Johnson Sathyanathan, president of the Synod of Pentecostal Churches in Coimbatore told Morning Star India: "It is a well-planned conspiracy against the Christian community, as the Hindu extremists know that it is not easy to approach the collector's office for such permissions.
"The time to get such approvals can stretch from a year and a half to many more years."
Orders were issued after complaints were apparently made by members of a paramilitary group, Rashtriya Swayamsevak Sangh, associated with the ruling Bharatiya Janata Party, the Hindu nationalist party.
A total of 10 churches have been affected by this order in the last two months - which Pastor Sathyanathan insisted have been doing ministry for years and people have never had a problem with before.
Since Narandra Modi took power in 2014, hostility against non-Hindus has become worse according to religious rights activists.
India is ranked 15 on Open Door's 2017 World Watch List.