The Council have one Minister, three Deputy minister and one Chief Secretary.

The internal units of Council are Department of Planning, Department of Marine Resources, Department of Maritime Security, Department of Science,Technology, Culture & Education, Department of International Development, Secretariat, Department of Personnel, Department of Civil Service Ethics, Department of Budget, Accounting & Statistic and Information Management Office.

Its Subordinate agencies are Coast Guard Administration and Ocean Conservation Administration.

In addition, for the mission of marine policy planning, marine resources investigation, marine scientific research, marine industry and human resources development , an affiliated institution named National Academy of Marine Research was established.