The ministry has decided to hand over to the National Investigation Agency (NIA) the investigation into the the killing of Ravinder Gosai in Ludhiana last month.
The decision has been taken following a recommendation of the Punjab government, the official said.
Gosai was shot dead by two motorcycle-borne assailants on October 17. He was the 'Sangh Pracharak' at the RSS Mohan Shakha in Ludhiana.
Four unidentified assailants also shot dead the leader of a lesser known Hindu outfit 'Hindu Sangarash Sena' Vipina Sharma in Amritsar in broad day light on October 30.
However, so far, the Punjab government has recommended for an NIA probe only Gosai's killing.