Japan launched its regulatory certification system for organic foods based on the amended JAS laws in June 2000, followed by the implementation of regulations on organic agricultural products and organic processed foods in January 2001 and with the implementation of the standards on organic animal husbandry and organic feed by the Ministry of Agriculture, Forestry & Fisheries in 2005, organic foods have been under integrated and systematic supervision. Certification of organic foods can be undertaken by registered accredited bodies (private certification bodies) or legal entities conforming to the regulations of the Ministry of Agriculture, Forestry & Fisheries. However, with the amendment of the JAS laws in March 2006, only legal entities conforming to the regulations of the ISO/IEC GUIDE 65 are eligible as certification bodies. Foreign organic products imported to Japan must be certified organic under JAS regulations and must be manufactured or produced by foreign manufacturers certified by local or foreign registered accredited organizations and distributed with the Organic JAS Mark affixed or through importers certified by local registered accredited organizations and distributed with the Organic JAS Mark affixed on the products. It can be implied from the Japanese case study that it necessary to reform the diverse agricultural products certification systems to set up an integrated certification system, and the restructuring of government organizations, reforms of environmentally-friendly agricultural products certification system and the integration of the organic food certification systems are needed in order to integrate the control of the standards and certification systems.