As far as the reform of Japan’s Agricultural Co-operatives is concerned, there are opposite voices such as “protection should be regarded as the premise of reform” and “disintegration is prior”. This paper aims to analyze the key problem that Japan agriculture meets, that is, the position of Agricultural Co-operatives in the structural reform and the relationship between Agricultural Co-operatives and the structural reform, so as to find out a middle- and long-term feasible solution to Japan’s Agricultural Co-operatives reform. The paper also examines important agricultural policies related to the structural reform in Japan after World War II. The future reform of Japan’s Agricultural Co-operatives wants administrative reforms in organizations and operation and stripping off its financial business so as to transform Japan’s Agricultural Co-operatives into organizations specialized in agricultural business in a middle term and competitive modernized agricultural organizations in a long term.