Executive Order No. 216, dated 17 November 1956 implemented Reorganization Plan No. 30-A reorganizing the Department of Agriculture and Natural Resources. Following this event, the Bureau of Fisheries which was reorganized on 16 January 1957, almost a decade after its creation. With this reorganization, functional divisions of the Bureau had been reduced from seven to five, namely: 1) Licenses and Regulations Division; (2) Marine Fisheries Division; (3) Fisheries Research Division; (4) Inland Fisheries Division; and (5) Administrative Services Division.
The Philippine Institute of Fisheries Technology had been transferred to the University of the Philippines. The seven secondary schools of fisheries in the provinces previously mentioned had been transferred to the Department of Education under the administration of the Bureau of Public Schools. On 20 March 1963, R.A. 3512 reorganized the Bureau of Fisheries and became the Philippine Fisheries Commission. In summary, the government fisheries agency had undergone three reorganization efforts during the 50s and the 60s.