This study aims to clarify the countermeasures required to protect Japanese nuclear power plants (NPPs) from grey-zone military threats—coercive actions that fall short of open armed conflict. It further examines whether replacing land-based NPPs with offshore floating nuclear power plants (OFNPs) could enhance deterrence and improve crisis response capabilities under Japan’s existing legal and institutional frameworks. A scenario planning approach was employed to explore high-impact, uncertain future scenarios involving grey-zone military threats to NPPs. Four representative scenarios were developed and analysed in relation to both Japanese government and plant operators, focusing on common failure points and feasible countermeasures. The analysis identified legal and institutional constraints that hinder the timely deployment of Self-Defence Forces, including requirements for prior Diet (Japan’s National Legislature) approval and rigid operational authorisations. Recommended countermeasures include shifting from a positive-list to a negative-list legal model; deploying drone countermeasures, such as high-power microwave systems; and reinforcing spent fuel pool buildings. OFNPs were found to offer both design-based and strategic advantages, including broad-area maritime surveillance and the ability to implement maritime security operations without Diet approval. This study clarified that mitigating grey-zone military threats to NPPs by 2035 will require integrated legal reform, technical enhancement, and strengthened operational preparedness. It also demonstrated that OFNPs offer advantages of deterrence and flexible crisis response, making them a promising alternative to conventional land-based NPPs in Japan’s evolving security environment.