• The Authority which comprises of Council of Ministers from the member countries responsible for transportation, is the highest policy organ. The Authority is responsible for overall policy direction and meets once every year.
  
• The Executive Board is an inter-governmental committee of senior officials of member states, which assists the Authority in formulating strategies for transport and trade facilitation, infrastructure development; and, harmonisation of national and regional policies.
  Chairmanship of the Authority and the Executive Board rotates among member countries. The Executive Board meets twice a year.
  
• The NCTTCA Permanent Secretariat is responsible for coordinating implementation of the NCTA and any other decisions and resolutions made by the Authority and Executive Board. The Secretariat is located in Mombasa, Kenya, and is headed by an Executive Secretary.
  

Besides the above three main organs, two Technical Committees, one on Infrastructure Development and the other on Customs and Trade, have been established and meet regularly.

In addition a Stakeholders Forum, comprising top-level representatives from public and private sector partner institutions, meet periodically to review operational matters and to agree on practical solutions, which they then implement.

Furthermore, national transit and trade facilittion committees are being established in each country.