Mitra will take over as the secretary after the present incumbent, G Mohan Kumar, completes his tenure on May 24, an order issued by the Department of Personnel and Training (DoPT) said.
The Appointments Committee of Cabinet (ACC) decided Mitra would till then function as an Officer on Special Duty in the Defence Ministry.
Mitra, 58, a 1982 batch Indian Administrative Service (IAS) officer of the West Bengal cadre, will have a fixed two-year tenure. This will be his posting in the Defence Ministry.
He also served a seven-year stint (November 2004 to July 2011) as a joint secretary in the Prime Minister's Office of Manmohan Singh.
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Shipping Secretary Rajive Kumar has been given the additional charge of the post of secretary, Road Transport and Highways.
Besides him, five new secretaries have been appointed in central government departments.
Mitra's batchmate Rashmi Verma, at present Textiles secretary, is the new Tourism secretary.
Petroleum and Natural Gas Additional Secretary Anant Kumar Singh will replace Verma.
Women and Child Development Secretary Leena Nair has been moved to the Ministry of Tribal Affairs in the same capacity.
Rakesh Srivastava, a 1981 batch IAS officer of the Rajasthan cadre, will replace Nair.
Srivastava is at present member secretary, National Commission for Backward Classes.
Electronics and Information Technology Secretary Aruna Sundararajan will hold the additional charge of secretary, department of Telecommunications, till the appointment of a regular incumbent, the order said.
The recently sidelined chief secretary of Jammu and Kashmir, B R Sharma, has been cleared for the post of additional secretary, Union Home Ministry.