Non-institutional measures often play an important role in the governance between technology and institutional system which have legal basis. In this study, we analyze the role of the “safety agreements” in Japan’s current regulation system of nuclear power plants (NPPs). In Japan, the national government regulates exclusively the safety of nuclear facilities based on the regulaions. But local governments also involve in the nuclear safety regulation de facto, to protect the publics’ safety and welfare. All the local governments in the siting areas concluded “safety agreements”, a gentleman-like agreement between local governments and power companies on safety issues. These Agreements contain various provisions, such as, the immediate notification procedures of accidents in NPPs, the access and inspection of NPPs after accidents, etc... However, these provisions don’t have a legal-binding of the power companies but, the local governors and local governments sometimes strongly assert the control for the restart operation of NPPs after the accidents utilizing the “safety agreements” as the pretext. This situation has sometimes been criticized by some experts who argue that the “safety agreements” have become an obstacle for stable NPPs operation and electricity supply. Since there are no studies which analyze the actual situations of local governments’ control on nuclear safety based on the “safety agreements,” we analyzed the situation by performing a qualitative survey and conducting a series of interview with personnel of the power companies and local governments. We found from our analysis that the “safety agreements” were utilized positively. For example, the inspection of NPPs by local government functions as an endorsement for the national regulation and assures public confidence. In this case the “safety agreements” promote and provide public acceptance on nuclear governance. However, the measures in these “safety agreements” could be over-extended in the political contexts because of the ambiguity and flexibility in the interpretation. In our paper, we would illustrate the merits and demerits of the role of local governments based on these “safety agreements” and suggest to improve the nuclear safety governance within the local governments’ capacity.