The Bureau of Fisheries and Aquatic Resources remained with the Ministry of Natural Resources for one decade until the agency was transferred to the jurisdiction of the Ministry of Agriculture and Food on 30 June 1984 in compliance with Executive Order No. 967 mandating the conversion of BFAR as a staff Bureau and integrating its Regional Offices with the Regional Offices of the Department of Agriculture. The agency’s staff function and integration of its regional offices to the Department of Agriculture was fully implemented on 30 January 1987 with the issuance of Executive Order 116 signed by former President Corazon C. Aquino.
Consequently, after a series of reorganizations in 1997, BFAR’s services were delivered through the nine (9) functional divisions: the Fisheries Policy Research and Economics Division, Fishery Resources Administration Division, Fisheries Development and Support Services Division, Aquaculture Division, Fisheries Resources Research Division, EEZ Exclusive Economic Zone Fisheries and Allied Services Division, Fishing Technology Division, Fisheries Regulation and Quarantine Division, and Post-Harvest Technology Division. It also has eight (8) fisheries technology centers under its wing: The National Marine Fisheries Development Center, National Brackishwater Aquaculture Technology Research Center, National Freshwater Fisheries Technology Research Center, Tanay Freshwater Experimental Station, Fisheries Biological Station Complex, National Fisheries Research Development Center, National Seaweeds Technology and Development Center and the Mindanao Freshwater Fisheries Technology Center.