<p>Ecotourism in Japan has evolved as a policy tool linking environmental conservation with regional revitalization under the Ecotourism Promotion Act. However, the relationships among certified regions or their collective significance within Japan’s ecotourism policy framework have received limited attention. This study provides a nationwide comparative analysis of 27 certified regions using official Overall Concept documents. Based on principal component analysis and K-means clustering, three ecotourism types were identified: the Regional Revitalization Type, characterized by depopulation, decline in primary industries, and local heritage resources; the Nature Conservation Type, associated with areas of high conservation value, visitor management, and interpretation; and the High-volume Tourism Type, representing established tourist destinations where ecotourism is incorporated into sustainable destination management. The findings show that certified ecotourism regions in Japan are not organized around a single model, but reflect diverse socio-ecological and place-based characteristics. This typology highlights the multiple roles of ecotourism and the importance of context-specific planning.</p><p><b>Clinical Trial Registration</b></p><p>Clinical trial number: not applicable. This study did not involve any clinical interventions or trials.</p>