Members of Hindu group, Bajrang Dal, allegedly barged into a church's prayer hall in the Hassan district of Karnataka state on Sunday and stopped the religious service midway, requesting the congregation to step out of the hall.
They claimed religious conversions were taking place there.
Video clips have appeared on social media showing members of Bajrang Dal engaged in heated discussions with Christian women.
"The incident happened Sunday. We reached the spot and warned both sides," police officer KM Yogesh told reporters.
The latest incident comes weeks before an Anti-Conversion Bill is likely to be passed by Karnataka's state government in the next legislative session, which begins on 13 December.
A separate incident of Bajrang Dal members vandalising a newly opened church was reported on Sunday in Delhi. The church in question was holding its first Sunday prayers when the incident took place, leaving one person injured.
Bajrang Dal is the youth wing of the Vishva Hindu Parishad, a popular Hindu organisation in India.
Delhi Police have filed an official complaint about the incident.