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This article will focus on the conundrum of building the political legitimacy while institutionalizing religious freedom which the newly established goisshin 御一新 government confronted. Liberation of "evil sects", which not only meant Christianity but also other religious sects such as fujufuse-ha of Nichiren school, was an issue which the Meiji state wanted to dodge. Western states demanded the lifting of the ban on Christianity but Japanese political leaders were vigilant against the idea. Reluctantly the Meiji state lifted the ban on Christianity in 1873 but they had started the institutionalization of Shinto as the state religion in advance. The government officials viewed that Christian faith and churches in Western countries were devised to prevent public mind from dissolution. They strived to establish an alternative version of religious authority in Japan instead of introducing the principle of conscientious freedom. However, on the other hand, a new generation of intellectuals raised the protection of the individual right of religious freedom as an urgent issue. I will analyze the diplomatic negotiations between the Western countries and the Meiji government officials, reports on the Western religious and educational systems in the Iwakura Mission records, voices of Buddhist and Shinto groups, and publications by leading intellectuals such as Nakamura Masao and Katō Hiroyuki so as to build a picture of how the concept of conscientious liberty was treated in such entangled contexts.