Negi, who retires on July 31, was Chief Minister Arvind Kejriwal's first choice for the top bureaucratic post after the AAP government took charge in its second term. However, the Centre had rejected the demand on the ground of lack of seniority.
A Delhi government spokesperson said Negi has been given the charge after getting the clearance of Lt Governor Najeeb Jung, which was seconded by a source in the Raj Niwas.
The government had alleged that the appointment was done without its consent.
Yesterday, the government also transferred and posted six IAS officers.
It appointed Dharmendra Sharma as Principal Secretary of the Finance Department as senior bureaucrat S N Sahai was transfered from the post and made the Chief Secretary of Goa.