58-year-old Kothari, a 1978-batch IAS officer from Haryana cadre, was serving as Secretary of Department of Administrative Reforms and Public Grievances, and Department of Pensions and Pensioners' Welfare.
He has taken over the charge from S K Sarkar, who retired yesterday.
Kothari will be responsible for taking decisions on personnel matters of government employees, Lokpal, transparency in governance and on the Right to Information (RTI) Act, among others.