The petitioners said that the affidavit filed by the BJP-led government "discloses that political groups linked to the Union were themselves involved in the communal crimes".
Union minister Smriti Irani said that it was up to the state governments to maintain law and order and prosecute crimes against citizens, including minorities.
Violent confrontations, ritual beatings, sudden threats now define what was earlier a peaceful environment to organise prayer meets in. Police and political support bolster such attacks.
In the latest in the rising instances of such communal attacks on Christians, the members of the right-wing group allegedly threatened to hang up pictures of Hindu goddess Saraswati in the convent school.