Mr Gupta, a 1971 batch IAS officer, is at present Secretary in the Ministry of Youth Affairs and Sports.
Official sources said here that he today took over as Officer-on-Special Duty (OSD) in the Ministry of Home Affairs (MHA) in the payscale of Secretary.
He would continue in that capacity till he takes over as Secretary of the Home Affairs Ministry when Mr Duggal demits office on March 31.
Mr Gupta will have a tenure of two years as Secretary.
He had worked in the MHA in the 90s as Joint Secretary in charge of Jammu and Kashmir when militancy was at its peak.
He had also served as Chief Secretary in Uttaranchal.
Mr Gupta is a native of Saharanpur in Uttar Pradesh.