The original mandate of MCS embodied in E.O. No. 392, is to serve as a leprosarium in Region IX. However, Department Order No. 375-5, dated July 26, 1994, also known as the Sanitaria Conversion and Development, a part of the DOH Hospital Upgrading Plan, further expanded the legal mandate of MCS. Under this Sanitaria Conversion Plan, MCS was tasked the following legal mandates:

A. To be the Sanitarium for the entire Mindanao area;

B. To upgrade to a 50-bed capacity general hospital with secondary capabilities, and

C.  To upgrade a Drug Rehabilitation Center for Western Mindanao

Mindanao Central Sanitarium, a government health facility, serving as the principal health care and health education resource venue for leprosy in the entire Mindanao area with the dual role of a general hospital to serve the general population along the East Coast of Zamboanga City.

Mindanao Central Sanitarium must provide health care services ranging from the care of Hansenites to that of the General Population, one that is designed to advance appropriate medical and health related services to all, especially the poor and marginalized sectors of society. In pursuit of this mission, the Mindanao Central Sanitarium will continuously upgrade its service capabilities to provide quality, affordable, and comprehensive health care services responsive to the changing needs of the people, by competent and committed health workers in partnership with the community.