How do major parties compete with each other and organize themselves in the multi-level political arenas in Japan? Using the survey data of Diet members and those of the prefectural assembly members, this paper argues that organizations of Japanese major parties are affected not only by the institutions of House of Representatives, but also by those of House of Councilors and those of local government. This paper finds an evidence indicating that the members of the House of Councilors and the members of prefectural assemblies take farther policy positions and have more autonomy from party leadership than the members of the House of Representatives, when other variables such as party affiliation and district characteristics are controlled. Though electoral reform of the House of Representatives which replaced SNTV with SMD have strengthened the leadership of major parties in Japan, the result suggests that institutions of the House of Councilors and those of local governments may counterbalance such trend.