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The NAFC started as the Rice and Corn Coordinating Council or RCCC in 1958 by virtue of Republic Act 2084.

It was tasked to oversee interagency activities on rice and corn production.In 1964, the RCCC was replaced by the Rice and Corn Authority (RCA) through Executive Order No. 62 under the Office of the President. Apart from overseeing the rice and corn production, it was also tasked to supervise its supply and distribution.

Two years later, the Rice and Corn Production Coordinating Council (RCPCC) replaced the RCA by virtue of Executive Order No. 50. For the first time, the government sought to harness community participation in the government's grain programs.

About three years later, the country's food requirement outgrew the effectiveness of the RCPCC. Thus, in 1969, the National Food and Agriculture Council (NFAC) was formed through Executive Order 183.

The NFAC was charged with the supervision and coordination of the government's food sufficiency program, which included for the first time, crops other than rice and corn. It also assisted the Department of Agriculture in the formulation of the goals, and defining the scope of the country's food and agricultural policies, plans and programs.

Three policy declarations transformed the NFAC significantly. In 1980, Executive Order 596 recognized the prime role of farmers in food production. Their participation in the NFAC was redefined and encouraged. The following year, Executive Order 754 expanded NFAC's functions to include non-agricultural concerns. In 1982, the DA through Executive Order No. 803 adopted the Integrated Area Management System approach in the delivery of inputs and services to the farmers. The NFAC assisted the DA in integrating and coordinating the provision of all agricultural goods to the farmers.

On January 30, 1987, the Agricultural and Fishery Council were established under Executive Order 116 and created as an advisory body at the regional, provincial, municipal, primarily to promote private sector participation in agricultural and fishery development through consultation, advocacy, planning, monitoring and project evaluation.

The PHILIPPINE COUNCIL FOR AGRICULTURE AND FISHERIES or PCAF was formed upon the consolidation of two agencies under the Department of Agriculture (DA): the National Agricultural and Fishery Council (NAFC) and the Livestock Development Council (LDC). The consolidation of these agencies is pursuant to Executive Order No. 366, Series of 2004 "Directing a Strategic Review of the Operations and Organizations of the Executive Branch and Providing Options and Incentives for Government Employees Who May Be Affected by the Rationalization of the Functions and Agencies of the Executive Branch."