CAF is organized into 6 departments and 1 center. Center is given a responsible for doing applied research and technology transfer, while departments take responsible for education and basic and applied research.

• Department of Aquatic Biology and Pathology

• Department of Applied Hydrobiology

• Department of Freshwater Aquaculture

• Department of Coastal Aquaculture

• Department of Aquatic Nutrition and Products Processing

• Department of Fisheries Management and Economies

• Centre for Aquaculture Promotion

• Administrative Office