This study identified areas suitable for offshore wind energy development in Japan based on a low probability of conflicts with stakeholders, such as fishery groups, shipping agents, and residents (minor conflict areas). Using geographic information systems, this study uses a two-stage approach. The first stage reviews Japanese zoning rules and excludes non-conforming areas with rules. The second stage examines case studies of stakeholder conflicts to identify minor conflict areas using three parameters, i.e., distance from the shore, shipping density, and existence of fishery rights, by considering local concerns regarding the seascape and conflicts resulting from shipping routes and fishery rights. Although previous studies have assessed massive offshore wind energy potential areas (> 140,000 km2) with various approaches, the areas that conform to the zoning rules (53,665 km2) and minor conflicts areas (7,213 km2 or 2% of Japanese territorial waters) are significantly limited. Furthermore, this study revealed that concerns regarding the seascape are a key issue inhibiting the expansion of bottom-fixed offshore wind turbines in Japan. Thus, the approach, which considers both zoning rules and stakeholder conflicts, can reduce the risk of offshore wind energy potential overestimation. For offshore wind energy capacity targets, relevant authorities should carefully examine both the zoning rules and stakeholders.