Mr Shah had said that if the BJP comes to power in Bihar, rioters would be hung upside down, a comment that drew sharp retorts from Bihar Chief Minister Nitish Kumar and his West Bengal counterpart Mamata Banerjee.
The MHA has asked all states to ensure law and order during the Hanuman Jayanti festival in the wake of communal violence in Bengal and Bihar during Ram Navami.
The Calcutta High Court order came on a PIL filed by the Leader of the Opposition in the West Bengal Assembly Suvendu Adhikari in connection with Ram Navami clashes in the state.
"We are keeping a watch on the situation at both places (Nalanda and Rohtas). It was not a failure of the administration. Some have deliberately caused this unrest as a part of the conspiracy," the CM told reporters.