LC Goyal took over today as India's new home secretary, in place of Anil Goswami, who was asked to go on Wednesday night for interfering in CBI investigations against a politician.
Mr Goyal, the former rural development ministry secretary, has been a joint secretary in the ministry during the previous UPA regime.
The government asked Anil Goswami to resign after he admitted to making a telephone call to the CBI on behalf of Congress leader Matang Sinh, who was arrested last week in the Saradha chit fund case.
Mr Goswami was left with no choice, sources said, as he confronted an unhappy Prime Minister Narendra Modi and the possibility of an unceremonious sacking before his two-year tenure was to end in July.
After being briefed on the controversy by Home Minister Rajnath Singh, PM Modi decided to take a tough stand in a 90-minute meeting with officials, sources said. Mr Goswami was asked to explain his actions - first to the home minister and then to the Prime Minister's Office.
The home ministry has said that Anil Goswami has taken voluntary retirement from service.
Sources in the PM's Office said the official's removal is meant to send out a clear message that the Modi government is ready to back bureaucrats but not those crossing the line.
The CBI alleges there were large, unexplained transactions worth Rs. 30 crore between Mr Sinh and Saradha, which need investigation.
Before that, top missile scientist Avinash Chander was removed as chief of India's Defence Research and Development Organization.