Sea level rise (SLR) due to climate change poses a serious threat to human populations in coastal areas. As a result, assessing the impacts of SLR and evaluating potential adaptations is essential. This study assesses the impacts of SLR and ocean tides on coastal Japanese prefectures by estimating the extent of potentially inundated areas, affected populations, and economic damages. The latest climate scenarios, tidal data, and shared socioeconomic pathways (SSPs) are used to estimate the SLR and its inundation effects at a resolution of 1 km. Economic damages are estimated following the methods outlined in the “Manual for economic evaluation of flood control investment (draft).” It was found that all impacts (inundated areas, affected populations, and economic damages) under RCP2.6-SSP1 are significantly smaller than those under RCP8.5-SSP5, suggesting the importance of mitigation efforts. In addition, the study evaluates the cost and effectiveness of protection and relocation adaptations using data on the cost of constructing dikes and the cost of relocating houses and infrastructure. While relocations due to SLR have not yet been undertaken in Japan, the relocation costs could be estimated based on the conventional scheme of community relocation for natural disasters such as life-threatening floods and tsunamis caused by major earthquakes. It was found that the costs of relocation can exceed those of protection under the current framework of Japanese relocation policies.