Pastor Allen Gobi's church, Family of Jesus and its 25 members have been meeting there since December 2018.
It is one of 38,000 churches across the state overseen by The Synod of Pentecostal Churches.
The pastor has told Christian charity Christian Solidarity Worldwide (CSW) that he had been "harassed" by police to obtain permission to conduct prayer meetings or face closure.
The threat was carried out on 24th March went ten police officers arrived as the prayer meeting was about to begin at 9:30am.
Pastor Gobi was taken to a police station where he was forced to sign a written admission that he had no permission to conduct prayer meetings in the property.
The charity was informed by local sources that the Hindu Munnani (Hindu Front) had submitted a petition to the police to take action against the church.
Tamil Nadu, a South Indian state famed for its Hindu temples, has seen a surge of targeted attacks by local Hindu extremist groups against people holding prayer meetings.
Nehemiah Christie, Director of Legislation & Regulations at the Synod of Pentecostal Churches in Tamil Nadu, said in a statement: "It is sad to see police officers whose duty is to uphold the Indian Constitution acting in a biased and discriminatory way.
"Their failure to uphold the rule of law emboldens the local fringe groups to target the Christian's right to worship. We are shocked to hear that this is happening in a state which has traditionally been tolerant of religious minorities.
"There were 29 incidents in the first 31 days of 2019. The Indian government must take serious measures to address police conduct and objectivity so as not to erode the confidence by the minority community, especially Christians."
CSW's Chief Executive Mervyn Thomas also called on officials to do more to protect Christians: "We continue to call on the Government to protect the civil rights of religious minorities to gather and pray.
"The right to manifest religion or belief in worship, observance, practice and teaching is fundamental to all. It is concerning to see that the police are interfering and harassing religious minorities based on spurious and malicious claims by hard-line groups.
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