The predecessor of the Fisheries Agency is the Fisheries Bureau of the Ministry of Agriculture and Commerce established in 1885. The Agency was reestablished in 1948 as an external bureau of the Ministry of Agriculture and Forestry to govern the administration of fisheries. Since then, the Agency has been involved in the promotion of the domestic fishing industry and negotiations on fisheries with foreign countries.

With the internationalization of the fishing industry, the scope of the Agency's work was expanded, and the Agency was organized into five departments in 1978: Fisheries Administration Department, Fisheries Promotion Department, Oceanic Fisheries Department, Fishing Port Department and Research Department. Currently, the Agency is organized into four departments: Fisheries Department, Resources Management Department, Resources Development Department, and Fishing Port Department.