The headquarters of the Fisheries Research Institute (FRI) is located in the city of Keelung in northern Taiwan. The Institute is composed of four administrative offices (Secretariat, Accounting, Personnel, and Civil Service Ethics) and four research divisions (Marine Fisheries Division, Aquaculture Division, Seafood Technology Division, Planning and Information Division).

　　To evaluate and carry out research, the FRI has also set up six research centers in strategic locations throughout Taiwan, namely, the Freshwater Aquaculture Research Center, Mariculture Research Center, Coastal and Offshore Resource Research Center, Tungkang Biotechnology Research Center, Eastern Marine Biology Research Center, and Penghu Marine Biology Research Center.

　　In addition, the FRI has four research vessels: R/V Fishery Researcher I, R/V Hai-Fu, R/V Hai-Chien, and H/V Hai-An. They are equipped with high-tech equipment to survey fisheries resources, fishing grounds, and the ocean environment.