The youth brigade, set up in 2002 by Yogi Adityanath who is now Uttar Pradesh Chief Minister, filed a complaint against Yohannan Adam, the pastor of the church, accusing him of converting Hindus to Christianity, a charge the pastor denied.
Police officer Anand Kumar Gupta said no prior permission was taken for the meeting, which was held ahead of Good Friday.
"We stopped the prayer meeting after a complaint was registered. A probe is underway and appropriate action will be taken if the charges are found to be correct," he said.
The incident took place in Dathauli in the district in eastern Uttar Pradesh. It borders Gorakhpur, the Lok Sabha constituency represented five times by Yogi Adityanath before he took over as the chief minister of Uttar Pradesh.
Mr Gupta said mass was held there quite often but as this time foreigners were involved, the Hindu Yuva Vahini suspected that conversion was taking place.
"The presence of US nationals indicates that innocent and illiterate Hindus were being converted by missionaries who lured them with money to change their religion," alleged Hindu Yuva Vahini leader Krishna Nandan, who surrounded the church with his supporters yesterday afternoon.
They dispersed after police promised a probe and adequate action even as the church authorities dismissed allegations of conversion.
"The charges are absolutely baseless. The people were attending a prayer meeting voluntarily. We prayed. Nothing else was done," pastor Adam said.
The Hindu right wing has been at loggerheads with Christian missionaries, accusing them of converting people through coercion and allurement.