After the Fukushima accident in 2011, approximately 160000 residents were forced to evacuate the site. The evacuation order has since been lifted and the Japanese government is now advancing a return strategy. As the return proceeds, deterioration of health indicators and measures in the municipalities around the nuclear power plant remains unchanged. This affected the local governments’ coronavirus disease (COVID-19) vaccination drive during the COVID-19 pandemic. In Japan, municipalities keep track of residents’ information and implement health-related measures. However, many residents evacuated the town, thus leaving their registered residence. With long-term evacuation and few returnees, it was difficult for government officials to constantly monitor the residents’ health. Therefore, there is an urgent need to maintain residents’ records and ensure that they receive health services without any gap. This report aimed to provide implications for post-disaster community health services and support as observed during the COVID-19 vaccination program at a disaster site.