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 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.

In 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. The NCBP now involves more government agencies such as the Department of Science and Technology (DOST), Department of Agriculture (DA), Department of Environment and Natural Resources (DENR) and Department of Health (DOH) to reflect the breadth and complexity of issues related to modern biotechnology. Other Departments and agencies which shall participate in biosafety decision making where appropriate, are the Department of Foreign Affairs (DFA), in promoting and protecting Philippine interests on biosafety in bilateral, regional and multilateral forums; the Department of Trade and Industry (DTI), in relation to biosafety decisions which have impact on trade, intellectual property rights, investments and consumer welfare and protection; the National Commission on Indigenous Peoples, in relation to biosafety decisions which have a specific impact on indigenous peoples and communities; and the Department of Interior and Local Government (DILG), in relation to biosafety decisions which have impact on the autonomy of local government units.