The Secretariat is responsible to the Council for the administration of the MEC and the conduct of the examinations. The Council Secretariat is headed by the Chief Executive who is the principal executive, chief administrative and academic officer. The present Chief Executive of the MEC is YBrs. Encik Adnan Bin Husin.

The Council Secretariat comprises two main sectors headed respectively by the Deputy Chief Executive 1 and Deputy Chief Executive 2. The sectors are as follows:

1. The Research, Item Buildingand Testing Sector
   1. Research and Examinations Policy Division
   2. Information Technology Management
   3. Science and Mathematics Division
   4. Social Science and MUET Division
   5. Security Printing Division
   6. Competency Building Division

This sector is responsible for matters related to syllabuses, item building, printing and supply of question papers, processing of examination results and data, standard fixing, awarding of certificates, research and training.

2. The General Administration, Finance and Management of Examinations Sector
   1. Competency Administration Division
   2. Personnel Management and Administration Division
   3. STPM & MUET Administration Division
   4. Security Management Division
   5. Finance Division

This sector is responsible for matters related to human resource, services, general administration, accounts, registration of candidates, administration of examination centres, marking of answer scripts, appointment of invigilators and examiners and security.

The Public Relations Unit, the Internal Audit Unit, and the Integrity Unit are directly responsible to the Chief Executive.

In the administration of examinations, the MEC is assisted by the Ministry of Education, State Education Departments , Ministry of Higher Education and all public institutions of higher learning.