Agricultural ecosystems are the largest managed ecosystem in the world. The sustainable development of agriculture is significant to the reversion of dramatic loss of biological diversity in the world. Globally Important Agricultural Heritage Systems (GIAHS) project launched by Food and Agriculture Organization (FAO) of the United Nations is among the global efforts to conserve and dynamically manage the specific agricultural knowledge system and landscapes. Ministry of Agriculture, Forestry and Fisheries (MAFF), Japan stressed the environmental concern of conventional farming practices in Japan in 1992. Noto Peninsula and Sado City were designated as two new GIAHS pilot sites in Japan as part of local level initiative to preserve the traditional agricultural systems in 2011. This paper reviewed the development process of sustainable farming in Japan and analyzed the challenges and new possibilities to its further extension. The current situation of various sustainable farming practices: such as farming with reduced input of chemical fertilizers and pesticides to conserve rich biodiversity, and organic farming, were reviewed. Emphasis was given to the sustainable farming practices in Hokuriku region, in particular, Ishikawa Prefecture and Sado City in Niigata Prefecture. Based on the recent official documents, reports and research papers, policy implication was brought forward. The challenges of sustainable farming practices and market valuation of sustainable farming products were analyzed. It was concluded that the environmental concerns of farmers and consumers are key to extend the sustainable farming practice in Japan. Conversion to bottom up policy making process paying attention to farmers' interest with involvement of multi stakeholders including government, researchers and private sectors is effective for sustainable farming extension.