NFRDI is organized into three research and development divisions, three support divisions, and four national research and development centers, which are strategically situated across the country.

• Aquaculture Research and Development Division or ARDD

ARDD focuses on the cultivation and farming of aquatic plants and animals, including breeding, feed and nutrition, aquatic animal health, farming systems and engineering, and technology business incubation for aquaculture.

• Capture Fisheries Research and Development Division or CFRDD

CFRDD conducts research on the harvesting of fish and other aquatic species from their natural environment. This includes ecological and economic studies of stocks, as well as the effects of fishing methods and gear on coastal and inland ecosystems, including the Exclusive Economic Zone (EEZ) and international waters. CFRDD also performs stock assessment studies within the jurisdiction of the 12 Fisheries Management Areas (FMAs).

• Fisheries Postharvest Research and Development Division or FPHRDD

FPHRDD focuses on postharvest and marketing studies, including fish handling and processing, product development, seafood safety and quality, trade of fish products, and technology business incubation for postharvest operations.

• Planning, Policy, and Information Division or PPID

PPID is responsible for formulating, monitoring, and evaluating the Institute’s periodic plans and programs, policy agenda, and information system. The division also develops strategic and operational plans and sets policy recommendation standards and guidelines.

• Training Division or TD

TD develops and conducts fishery training programs for internal and external stakeholders and produces multimedia information products for informed decision-making and technology transfer.

• Finance and Administrative Division or FAD

FAD manages administrative and financial tasks, such as human resources, property, general services, records, cash flow, budgeting, and accounting.

• Freshwater Fisheries Research and Development Center or FFRDC

Located in Butong, Taal, Batangas, FFRDC conducts research development and extension services in freshwater fisheries.

• Marine Fisheries Research and Development Center or MFRDC

MFRDC focuses on research development and extension services in marine waters fisheries. It also undertakes socio-economic studies on livelihood and income diversification program and applied research projects in coordination with academe and other research institutions. The Center is located in Guian, Eastern Samar.

• Brackishwater Fisheries Research and Development Center (BFRDC)

BFRDC, which is located in Lala, Lanao del Norte is responsible for research development and extension services in brackishwater fisheries, develops grow-out technology appropriate for brackishwater species and improvement of quality seed supply and broodstock.

• Fisheries Biotechnology Center (FBC)

FBC performs research and development, and extension services in fisheries biotechnology with the goal of advancing the management and utilization of aquatic resources. It is currently located at Central Luzon State University, Science City of Munoz, Nueva Ecija.