The Department is divided into three Directorates namely, Directorate of Higher & Technical Education, Directorate of School Education & Literacy, and Directorate of Educational Research and Training at the State Level.

Directorate of Higher and Technical Education (DHTE):
All matters relating to higher education including scholarships, NCC and NSS are under the DHTE. The Directorate of Higher & Technical Education plays a very important role in administration, governance and supervision of different activities relating to Higher Education including College & University Education, Technical Education, Professional Education and Vocational Education in the State of Meghalaya. The activities are aimed at Human Resource Development and generation of technical man power according to the need of the Society. All Govt. Institutions are under its direct control while the Non-Govt. Institutions that receive grant-in-aid from the Govt. in the form salary of the teachers etc. are under the direct control of the Governing Body or Managing Committee of the institution.

Directorate of Educational Research and Training:
In order to provide direction and thrust to School Education & Teacher Education the State Council of Educational Research was set up in Directorate of Public Instruction (DPI). In 1997 the Directorate of Public Instruction was trifurcated and SCERT became a fully fledged Directorate of Educational Research and Training (DERT) with its own Director. The main functions of this Directorate is to help bring about qualitative improvement in the field of School Education through quality Teacher Education Programmes, as the Government firmly believes that quality in school education greatly depends on professional competence of teachers.The District Institute of Education and Training (DIET) at the Districts are the Units of DERT.

Directorate of  School Education and Literacy:

The “Directorate of School Education and Literacy” which was earlier known by the “Directorate of Mass and Elementary Education” and was entrust to take care of Elementary Education, including adult and non-formal education only was officially renamed vide notification dated 17th December, 2009 whereby the name has been changed to “Directorate of School Education and Literacy” and the Directorate has been entrusted to look after Pre-primary schooling, Primary and Upper Primary Education, the Adults and Non-Formal Education and other new levels which was included in this Directorate are the Secondary and Higher Secondary Education.