The visa application of the Baptist World Alliance leader was rejected by the Consulate General of India in Johannesburg, South Africa, on Wednesday, a move which was criticised by the Christian community in poll-bound Meghalaya.
Elections to the 60-member Meghalaya assembly will be held on February 27 and votes will be counted on March 3.
"The Congress has no agenda but is only trying to force the church into politics by trying to mislead and misuse the church for political reasons," BJP spokesperson Nalin Kohli told reporters in Shillong.
Chief Minister Mukul Sangma alleged that the central government not giving permission to Paul Msiza to attend the sesquicentenary celebrations organised by the Garo Baptist Convention in the Garo Hills shows the hidden agenda of the government.
The Garo Baptist Convention is celebrating 150 years of the Baptist church entering Garo Hills at Rajasimla in 1867.
However, Mr Kohli said the BJP does not decide on visa matters. "Visa authorities follow rules set up by respective governments in every country. In India, it was the Congress that made the visa rules because they ruled the country for 55 years and those rules have to be adhered to irrespective of any community or religion," Mr Kohli said.
The Baptist World Alliance is a worldwide alliance of Baptist churches and organisations, formed in 1905 in London.