The NECO administration is organised into nine departments, headed by Directors, and the Office of the Registrar. While the Departments are organized into Divisions composed of Units.
At the head of the Management of NECO is the Registrar who, under section 9(1) of its enabling Act shall be appointed by the President, on the recommendation of the Minister. Under subsection 2 of the section, the Registrar shall be the Chief Executive of the Council and shall be responsible for the execution of the policy of the Council and manage its affairs under its direction.
The Registrar and his team of Directors are accountable to the Governing Board which is headed by a Chairman and has 17 other members, including the Registrar, drawn from a number of stake holding institutions.