The Mandate of the Ministry Headquarters is to set the agenda for health in Malawi in collaboration with stakeholders. The Minister of Health provides Government’s Policy directions on health matters. The Secretary for Health is responsible for the overall functioning of the health sector supported by health professionals, technical, administrative, financial, human resource, procurement and other expert staff.

The Ministry Headquarters  is responsible for developing, reviewing and enforcing health and related policies for the health sector; spearheading sector reforms; developing and reviewing standards, norms and management protocols for service delivery and ensuring that these are communicated to lower level institutions; planning and mobilizing health resources for the health sector including allocation and management; advising other ministries, departments and agencies on health related issues; providing technical support for supervision; coordinating research; and monitoring and evaluation.

Ministry executes these functions through its fourteen directorates, these are:

1. Directorate of Administration

2. Directorate of Finance

3. Directorate of Human Resources 

4. Directorate of Clinical Services 

5. Directorate of Nursing & Midwifery Services

6. Directorate of Preventive Health Services 

7. National Public Health Institute of Malawi

8. Directorate of Health Technical Support Services (HTTS)

9. Directorate of Planning & Policy Development (P&PD)

10. Directorate of Health Research 

11. Directorate of Reproductive Health 

12. Directorate of Safe Motherhood

13. Directorate of Nutrition

14. Quality Management Directorate