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The overlapping jurisdictions and universalizing rhetoric of the Occupation created a situation in which the concept of religious freedom had to change. Two governments were in charge of the same territory and population, meaning that rights had to come from someplace beyond the state. Moreover, the occupiers did not trust Japanese political leaders to continue to guarantee religious freedom once the Occupation ended. The occupiers found a solution to this twofold enforcement problem through an outreach program premised on the intertwined notions that all humans were inherently religious and that religiosity preceded (or superseded) national citizenship. Through popular media and public-facing outreach lectures explaining the American-drafted constitution that had been promulgated in November 1946, Japanese legal experts and scholars of religion helped the occupiers frame religious freedom as innate, universal, and unquestionable. But while religious freedom appeared in this discourse as a universal human right rather than as a parochial civil liberty, stakeholders continued to discriminate between what they saw as "good" and "bad" types of religion, effectively circumscribing the scope of the supposedly inalienable right. Simultaneously, American political leaders weaponized the ostensibly pacifistic concept of religious-freedom-as-human-right, making it a powerful ideological tool for their battles against "godless communism" worldwide.

Scholars of religion eagerly took up the Occupation mandate to foster "a desire for religious freedom" in the Japanese populace. These efforts can be seen in three postwar concepts that have deeply structured the postwar academic study of Japanese religions, but that have also had global reach. The concept of "new religions" was born out of Occupation-era collaborations between representatives of marginal religious movements, military government officials, and scholars of religion as a way of protecting the rights of some minority religions by avoiding pejorative terms such as “superstition” (meishin), “lascivious heresies” (inshi jakyō), and “upstart religions” (shinkō shūkyō). In translation, the concept of “new religions” went on to become a broadly accepted category in the global religious studies academy. Similarly, the postwar notion of "Buddhist war responsibility" helped to structure the widespread expectation that Buddhism, more than other religions, is inherently politically progressive and indisputably pacifist. Finally, the concept of "State Shintō" served as an early example of a "perversion of faith," a problematic framing device that dominates "countering violent extremism" initiatives to this day.