Shekhar Dutt belonged to the 1969 batch of Indian Administrative Service from Madhya Pradesh cadre. Shekhar Dutt became the Service Commission Officer in the Indian Army. He was awarded the Sena Medal for the gallantry during the Indo-Pakistani War of 1971. Shekhar Dutt was Divisional Commissioner of Raipur Revenue Division in 1985-1989.
Shekhar Dutt held in various prestigious posts in the Government of Madhya Pradesh, including Principal Secretary in the Department of Tribal and Scheduled Caste Welfare and Principal Secretary, Departments of School Education, Sports and Youth Welfare.
Shekhar Dutt was appointed as the Secretary of the Department of Ayurveda, Yoga, Naturopathy, Unani, Siddha and Homeopathy in the Ministry of Health and Family Welfare of India. Shekhar Dutt was a Director in many Public Sector undertaking boards such as Bharat Electronics Ltd., Bharat Earth Movers Ltd, Mazagaon Docks Ltd, Bharat Dynamics Ltd, Garden Reach Shipbuilders and Engineers Ltd, and Goa Shipyard Ltd.
Shekhar Dutt also served as the Director General of the Sports Authority of India. Shekhar Dutt played a role in the hosting of the Afro-Asian Games in Hyderabad in November 2003.
Later, Shekhar Dutt became the Joint Secretary in the Department of Defence Production from 1991 to 1996. He later took over as the Defence Secretary of India in the year 2005. In the year 2007, June, Shekhar Dutt retired as the Defence Secretary. Later he was appointed as the Deputy National Security Advisor for a two-year term. In September 2009, Shekhar Dutt was named to the Board of Trustees of De Sales University.
Shekhar Dutt is an avid writer also. He wrote the non fiction book "Reflections on Contemporary India". This was launched by the President of India, Pranab Mukherjee on 11th February 2014.