Heads or representatives from the affiliated institutions serve on the Board of COSTECH, which is commonly known as the Commission. Members of the Commission also include professors from national universities and policy makers from Ministries of both Union and Zanzibar Government. The Commissioners are triennially appointed by the Minister responsible for science and technology and the Chairperson of the Commission is a Presidential appointee. Some of the Commission members constitute an Executive Committee, which is a statutory organ of the Commission to which the Commission can delegate, any of its functions. As the governing authority of COSTECH, the Commission gives broad directives and guidelines to the Secretariat and its various R&D Advisory Committees.

The composition of the Commission has members representing all sectors of the economy, Deans/Directors of faculties and institutes that deal with R&D activities and representatives from Ministries of both the Union Government and Government of Zanzibar that directly affect R&D activities in the country. Thus, all key national economic sectors, which include: agriculture and livestock, public health, forestry, fisheries, marine sciences, minerals, industry and energy and wildlife are represented. Part III, Section 14 of the COSTECH Act establishes an Executive Committee which is a statutory organ of the Commission to which the Commission may delegate any of its functions. As per Section 14 Subsection 2 of the Act, the Commission established Standing Committees known as Audit Committee, Finance, Planning, and Administration Committee, and Estate Committee to assist in its oversight role on audit, financial, Human Resource and Real Estate Matters.