Medical Stores Department (MSD) is an autonomous government under the Ministry of Health. It was established by the Parliamentary Act No. 13 of 1993 and later amended by the Written Laws (Miscellaneous Amendments) (Act No. 4) of 2021. This amendment grants MSD corporate status, including perpetual succession, a common seal, and the ability to perform all actions legally allowed for a corporate body, as outlined in Section 15 of the Act.

The Written Laws (Miscellaneous Amendments) (No. 2) Act, 2024 amended the Act to authorize the Department to invest subject to directives issued by the Treasury Registrar occasionally. As an autonomous department, MSD is responsible for developing, maintaining, and managing an efficient and cost-effective production, procurement, storage, and distribution of approved medicines and medical supplies required by all public health facilities.

The Board of Trustees is the highest decision-making body that governs and sets the direction of MSD on behalf of the Ministry of Health. It comprises nine (9) members appointed every three years. The President of the United Republic of Tanzania appoints the Chairman, while the Minister responsible for health appoints the other eight (8) members. The Director General serves as the Secretary to the Board but has no right to vote.

To effectively implement its responsibilities, the Board operates through three committees: the Audit and Risk Management Committee, the Technical Services Committee, and the Finance and Administration Committee. The Board delegates the day-to-day management of the Department to the Director General, appointed by the President of the United Republic of Tanzania.

The department's administrative functions and operations are carried out by and through the Executive Management Team (EMT). The EMT comprises the Director General, Director of Administration and Human Resources, Director of Finance, Director of Logistics and Operations, Director of Procurement, and Director of Information and Communication Technology. The Chief Legal Counsel serves as Secretary to the EMT.

The Medical Stores Department operates through ten zonal stores in Dar es Salaam, Mwanza, Iringa, Kilimanjaro, Mbeya, Tabora, Dodoma, Tanga, Mtwara, and Kagera.