Recent studies have highlighted that flooding can influence population dynamics. However, existing estimates of future flood damage primarily consider population changes driven by births, deaths, and migration unrelated to flooding. As a result, the potential impacts of flood-induced population movements (FIPMs) on future flood damage costs remain largely unexplored. This study evaluated the impacts of FIPMs on future flood damage costs in Japan, a country that faces flood risk and population decline. We develop a methodological framework that uses statistical causal inference to quantify FIPMs, integrates these estimates into future population and land-use projections, and evaluates future flood damage costs under scenarios of climate and land-use change. The results indicate that incorporating FIPMs leads to only modest changes in estimated flood damage costs at the national level (generally below 1 %), and similarly modest impacts at the prefectural level, except for a few prefectures with changes of approximately 2 %. However, greater variability is observed at the municipal level, with approximately 10 % of municipalities experiencing changes exceeding 1 % and some municipalities showing reductions in estimated flood damage costs exceeding 10 %. These findings highlight the importance of accounting for FIPMs in flood risk management frameworks and policy evaluations.