Japan is a disaster-prone country and natural disasters could happen under COVID-19. Shelter management is especially important because many people evacuate there and there’s high risk of spreading infection. In order to establish feasible countermeasures in shelters, we conducted a survey about the current situation of preparation and experience of shelter management in Japanese local governments under COVID-19. From the answer of 346 municipalities, we found that some municipalities took measures against COVID-19 such as adding new shelters and conducting the training, and these proactive measures were very useful. However, due to the addition of infectious disease control work, it became clear that it would take time and difficulty at reception, and that it would be even more difficult to identify evacuees with the recommended distributed evacuation. These results can be useful in proceeding consideration of better shelter management under COVID-19.