SEAFO comprises of the Commission, the Scientific Committee (SC), the Compliance Committee (CC) and the Standing Committee on Administration and Finance (SCAF), and the Secretariat. 

The Commission has an oversight responsibility of the Organisation. The Scientific Committee provides scientific advice on the status of marine resource and on harvesting. The Compliance Committee provides the Commission with information, advice and recommendations on the implementation of, and compliance with, conservation and management measures. The Standing Committee on Administration and Finance is responsible for advising the Commission on budgetary and administrative matters of the Organization. The SEAFO Secretariat is based in Swakopmund, Namibia and is considered the administrative headquarters of the organization.