Administration of Jaintia Hills District is headed by the Deputy Commissioner. He also acts as the executive head as well as judicial head of the district. Deputy Commissioner is aided by a number of officers like Additional Deputy Commissioner, Sub-Divisional Officers of Civil Sub-Divisions and Extra Assistant Commissioners to assist him in different type of activities. As the executive head the Deputy Commissioner plays a vital role in coordinating with all developmental heads of the district for all round developmental activities. The District Planning Officer is assigned to see, formulate and release of fund for development scheme. There also exists the District Rural Development Agency (DRDA) and the Deputy Commissioner is the chairman of the said agency. The Project Director is the functional head of the agency. All schemes of rural development are implemented by Block Development Officers and the necessary funds are routed through this agency.

Maintenance of law and order is another important aspect of administration of Jaintia Hills District to give proper security and to safeguard the lives and properties of the citizen. In this regard the Deputy Commissioner acts as the District Magistrate for maintenance of law and order in the district. The District Magistrate is assisted by Additional Deputy Commissioner, Sub-Division Magistrates and other Executive Magistrates. Moreover, he also keeps close link with police department. The Superintendent of Police is the head of the Police Administration.

In revenue matter the Deputy Commissioner is assisted by Additional Deputy Commissioner of Revenue and other Revenue and Enforcement staff. There is constitutionally recognized Jaintia Hills Autonomous District Council in Jowai. Hence all types of revenue collection like settlement of Hats (Bazaar), Ghats, Ponds, Ferries, Professional tax are directly dealt by District Council, except matters like acquisition of government land, encroachment of government land, allotment of land to central department, payment of compensation money, etc.

Further, Deputy Commissioner plays a key role during natural disaster periods like flood, earthquake, landslide, cyclones or storm damage or fire incidences. The Deputy Commissioner generally takes prompt action whenever the situation arises in any part of the district, and provides assistance to the victims according to the nature of damage. Besides all these the Deputy Commissioner being the head of the district also holds the post of Chairman of various committee, colleges, schools, banks, etc. The United Khasi-Jaintia Hills Autonomous District Council came into existence on 27th of June, 1952 after being formally inaugurated by the then Governor of Assam. Administrative set-up of Jaintia Hills District includes two Sub-Divisions, five Blocks and 450 villages.