The Secretariat is the executive Organ of the Community. It ensures that the regulations and directives adopted by the Council of Ministers are properly implemented, and provides the Council of Ministers with strategic recommendations.
At the head of the EAC Secretariat is the Secretary General.
The Secretary-General is the principal executive and accounting officer of the Community as well as the Secretary of the Summit; he/she is appointed by the Summit for a fixed five-year, non-renewable term.
The four Deputy Secretaries-General deputise and support the Secretary-General in the management and executive direction of the EAC Secretariat. They are appointed by the Summit on recommendations of the Council and on a rotational basis. Each Deputy Secretary-General can serve a maximum of two three-year terms.
The Counsel to the Community is the principal legal adviser to the Community.
The health sector in EAC is organized into two (2) main distinctive spheres that are health programmatic issues and health research issues that are coordinated by EAC Health department and East African Health Research Commission (EAHRC) respectively.