<p>This study examines how differences in municipal administrative capacity influence adaptive governance in disaster response, particularly focusing on relationships with NPOs. This research analyzes contrasting approaches to adaptive governance through a comparative case study of two adjacent municipalities in Saga Prefecture, Japan: Omachi Town (population: 6,245) and Takeo City (population: 48,637). Both municipalities experienced floods caused by the same rainfall events in 2019 and 2021 and had limited prior experience with NPO collaboration. The study finds that the small municipality (town) demonstrated stronger adaptive governance by deeply embedding external NPOs into their administration to compensate for limited capacity, while the medium-sized municipality initially showed reluctance toward NPOs but later developed equal partnerships with NPOs. There are two reasons why the small town appeared to be adaptive. First, the small town lacked the administrative capacity to respond to disasters, so they had no choice but to adapt. Second, an official who was dispatched from the prefecture to the town as a liaison—this official later worked as the deputy mayor of this town—instructed the town staff that they needed to develop the capacity to accept assistance. While more robust adaptive governance is generally considered preferable for disaster response and recovery, there are inherent risks: over-reliance on NPOs and the tendency for nationwide NPOs to shift their resources when disasters strike elsewhere. Although this study is limited to the cases of only two municipalities, it provides contrasting valuable insights for the practice of adaptive governance.</p>