NMET has two-tier structure. The overall control, periodical reviews and policy directions of the Trust vest with the Governing Body (GB) and the Executive Committee (EC) is managing, administering and supervising the day-to-day activities of the Trust. The GB is chaired by Union Minister In-charge, Ministry of Mines and having members from Union Ministries of Coal, Petroleum & Natural Gas and Atomic Energy. Besides, Minister In-charge of Department of Mines & Geology from Six State Governments are also members of GB.

The EC is chaired by the Secretary, Ministry of Mines and having representatives from Ministry of Coal, Petroleum & Natural Gas and Atomic Energy. The representatives from four State governments are also members on rotation basis.

A Technical-cum-Cost Committee (TCC) evaluates the technical as well as cost parameters of the mineral exploration project proposals submitted by various Notified Exploration Agencies (NEAs). The TCC comprises the domain experts from various central/State Govt. Organizations. The TCC recommends the suitable proposals to EC for approval.