The National Codex Organization (NCO) alternately chaired by the Secretary of Agriculture and co-chaired by the Secretary of Health is a body composed of representatives from Philippine government agencies, non-government organizations and the industry sector with an interest in the nature of CODEX. It serves as an advisory body to the government on the implications of various food standardization and food safety issues arising from the work of Codex Alimentarius Commission (CAC) to protect the health of the consumers and ensure fair trade practices.

The Management Support Office (MSO) is currently housed at DA-FDC which coordinates the activities of the Executive Council, the Technical Committee and Sub-Committees or Task Forces of the National Codex Organization. It monitors the country positions in accordance with national policies and reflect national interest and capabilities.