Agriculture, forestry, fisheries and food industry products have been the foundation of the Japanese diet while providing Japanese society with the basis for living and cultural activities. Nevertheless, along with the progress of the Japanese economy, agriculture, forestry, and fisheries sectors have experienced a considerable decline in production and employment. The Japanese government has adopted various measures to reverse the decline of Japan's food self-sufficiency ratio under the Basic Law on Food, Agriculture and Rural Areas enacted in 1999. Comprehensive economic analyses of the situations of agriculture, forestry, fisheries and their related industries are necessary to cope with structural problems facing Japanese primary industries. This study examines the regional economic structure in Japan using input-output tables from segmented agriculture, forestry, fisheries, food and related industries. The study employs skyline analysis, analysis of the interregional trade balance, and structural decomposition analysis to identify present issues related to Japanese primary industries. Results reveal that interregional trade among metropolitan and local regions is a major determinant of agriculture, forestry, fisheries and food industries production. The decline in interregional trade in the 1990s has adversely affected the production of primary industries in Japan. JEL Classification: C67, O13