The Authority operates under the ministerial responsibility of the Ministry of Port, Harbour and railways and has a three-tier organizational structure, viz:
        .The Governing Board:
It is made up of institutional representation of various importers and exporters as well as government agencies responsible for maritime trade and transport. The Governing Board works through its technical Committees of Finance & Administration. Freight & Logistics and Ports & Infrastructure for the Achievement of its objectives.
        .The Import/Export Shipper Committees:
These are mainly made up of private sector importers and exporters from small scale to large scale. who meet regularly to discuss common shipping problem affecting the shipping industry in Ghana. There are six shippers committees in the country based in Accra, Takoradi, Kumasi Sunyani, Tamale and Bolgatanga / Bawku. These Committees are chaired by selected members of the Board of Directors.
        .The Secretariat:
The Authority's Secretariat is managed by a group of skilled and seasoned professionals directed by a Chief Executive Officer. The staff apply their skills, professional expertise and knowledge in providing solutions to the myriad of the problem encountered by the Ghanaian shipper on a daily basis. As repository of maritime data and information, the Secretariat also provides relevant inputs to government for informed policy decisions. The three branches of the Secretariat have been strategically located in Kumasi, Takoradi and Tema to ensure that its services are reached by its numerous clients. The Secretariat works through six functional departments, namely Freight, Logistics & Research, Shipper Services, Management Information Systems. Finance, Public Relations and Human Resource & Administration. These are supported by the legal and Audit units.