Japan experienced natural hazards during the COVID-19 pandemic as some other countries did. Kumamoto and Kagoshima prefectures, including many other parts of southern Japan, experienced record-breaking heavy rain on 4th July 2020. While many countries were affected by compound hazards, some cases such as the Kumamoto flood did not cause a spike of the COVID-19 cases even after going through massive evacuation actions. This study aims to understand how COVID-19 made an impact on people’s response actions, learn the challenges and problems during the response and recovery phases, and identify any innovative actions and efforts to overcome various restrictions and challenges through a questionnaire survey and interviews with the affected people. With an increase in the risk of compound hazards, it has become important to take a new, innovative, and non-traditional approach. Proper understanding and application of adaptive governance can make it possible to come up with a solution that can work directly on the complex challenges during disasters. This study identified that a spike of COVID-19 cases after the disaster could be avoided due to various preventive measures taken at the evacuation centers. It shows that it is possible to manage compound hazard risks with effective preparedness. Furthermore, during emergencies, public-private-partnership as well as collaboration among private organizations and local business networks are extremely important. These collaborations generate a new approach, mechanism and platform to tackle unprecedented challenges.