Prime Minister Jawaharlal Nehru inducted Mukherjee into the Interim Central Government as a Minister for Industry and Supply on 15 August 1947. Mukherjee began to have differences with Mahasabha after the assassination of Mahatma Gandhi, in which the organisation was blamed by Sardar Patel for creating the atmosphere that led to the killing. Mukherjee suggested the organisation suspend its political activities. Shortly after it did, in December 1948, he left. One of his reasons was the rejection of his proposal to allow non-Hindus to become members. Mukherjee resigned along with K.C. Neogy from the Cabinet on 8 April 1950 over a disagreement about the 1950 Delhi Pact with Pakistani Prime Minister Liaquat Ali Khan.