In 1972-1973, the country was beset by rice production shortfalls resulting from the series of typhoons and floods and fertilizer shortages spawned by the oil crisis. The resulting four-fold drop in rice production prompted the government to directly intervene in the operations of the fertilizer industry through the issuance of Presidential Decree (P.D.) No. 135 dated 22 February 1973, creating the Fertilizer Industry Authority (FIA).


                Fertilizer and pesticide are vital agricultural inputs in food production and must be supplied in adequate quantities at reasonable costs at all times. The fertilizer and pesticide industries have much in common in terms of clientele, distribution channels, system of application in farmers' fields and technical supervision by the same farm management technicians under the government's food production program. In view hereof, the government abolished the FIA and created the Fertilizer and Pesticide Authority on 30 May 1977 by virtue of P.D. 1144 and attaching it to the Department of Agriculture


                With the issuance of Executive Order No. 165 om May 5, 2014, the FPA was transferred to the Office of the President under the Office of the Presidential Assistant for Food Security and Agricultural Modernization (OPAFSAM)


                On September 17, 2018, President Rodrigo Roa Duterte issued Executive Order No. 62, once again transferring FPA from the Office of the President to the Department of Agriculture.