Khuntia will succeed Arvind Jadhav, who will be retiring from service on superannuation, a government notification said.
A 1981-batch officer, Khuntia has been appointed on repatriation from central deputation.
Jadhav, a 1978-batch IAS officer, was appointed as Chief Secretary on December 31, 2015.
He was to retire on June 30, but was given an extension of three months