Opposition leader Mallikarjun Kharge made the charge in the Lok Sabha, saying: "Where the BJP is in majority, more communal violence is reported from there."
Furious BJP MPs were up on their feet shouting slogans against Kharge the moment he made the statement.
Minister of State for Home Kiren Rijiju dismissed the claim and said records do not support the allegation.
"I think that is not a fair comment by the opposition leader," he said, adding that incidents of communal violence had actually come down since the BJP-led government took power last year.
He also dismissed Trinamool Congress' Saugata Roy's allegation that most incidents of communal violence were reported from Samjwadi Party-ruled Uttar Pradesh.