The Philippines is the first ASEAN country to initiate a biotechnology regulatory system with the issuance of Executive Order No. 430 in 1990, which established the National Committee on Biosafety of the Philippines (NCBP). The countries biosafety regulatory system follows strict scientific standards and has become a model for member-countries of the ASEAN seeking to become producers of agricultural biotechnology crops.

In 1987, scientists from the University of the Philippines Los Banos (UPLB) and the International Rice Research Institute (IRRI), the Quarantine Officer of the Bureau of Plant Industry (BPI), and the Director for Crops of the Philippine Council for Agriculture, Forestry and Natural Resources Research and Development (PCARRD), recognizing the potential harm of the introduction of exotic species and genetic engineering, formed a committee and formulated the biosafety protocols and guidelines for genetic engineering and related research activities for UPLB and IRRI researchers. The committee went on to draft a Philippine biosafety policy, which was submitted to the Office of the President. On October 15, 1990, recognizing the potential for modern biotechnology both in improving the lives of the people and in creating hazards if not handled properly, President Corazon C. Aquino issued Executive Order 430 creating the National Committee on Biosafety of the Philippines (NCBP) that will formulate, review and amend national policy on biosafety and formulate guidelines on the conduct of activities on genetic engineering. The NCBP is comprised of representative of the Departments of Agriculture (DA); Environment and Natural Resources (DENR); Health (DOH); and Science and Technology (DOST), 4 scientists in biology, environmental science, social science and physical science; and 2 respected members of the community. On July 16, 2001, President Gloria Macapagal-Arroyo issued the Policy Statement on Modern Biotechnology, reiterating the government policy on promoting the safe and responsible use of modern biotechnology. On April 3, 2002, Department of Agriculture Administrative Order No. 8, Series of 2002 was issued implementing the guidelines for importation and release into the environment of Plants and Plant Products Derived from the Use of Modern Biotechnology. On March 17, 2006, President Gloria Macapagal-Arroyo issued Executive Order No.514 Establishing the National Biosafety Framework, prescribing guidelines for its implementation, reorganizing the National Committee on Biosafety of the Philippines, and for other purposes. On December 8, 2015, the Philippine Supreme Court declared DA AO8 null and void and any application for contained use, field testing, propagation and commercialization, and importation of GMOs was temporarily enjoined. In response to the nullification of DA AO8, the Technical Working Group composed of representatives from the Departments of Agriculture (DA), Science and Technology (DOST), Environment and Natural Resources (DENR), Health (DOH), and Interior and Local Government (DILG) drafted the Joint Department Circular No. 1, Series of 2016 (JDC No.1, S2016) titled 'Rules and Regulations for the Research and Development, Handling and Use, Transboundary Movement, Release into the Environment, and Management of Genetically-Modified Plant and Plant Products Derived from the Use of Modern Biotechnology'. There were series of meeting and five public consultations conducted before the JDC No.1, S2016 was approved and signed by the Secretaries of the abovementioned agencies on March 7, 2016 and took effect on April 15, 2016. Under this Circular, more government agencies were involved such as the Department of Science and Technology (DOST) to regulate applications for contained use and confined test of regulated articles; Department of Agriculture (DA) to evaluate applications for field trial, commercial propagation and transboundary movement of regulated articles; Department of Environment and Natural Resources (DENR) to evaluate environmental risks and impacts of regulated articles; Department of Health (DOH) to evaluate of environmental health impacts of regulated articles; and Department of the Interior and Local Government (DILG) to supervise public consultation during field trial.