To address the impacts of future land changes on biodiversity and ecosystem services, land-use scenarios have been developed at the national scale in Japan. However, the validation of land-use scenarios remains a challenge owing to the lack of an appropriate validation method. This research developed land-use maps for 10 land-use categories to calibrate a land-change model for the 1987–1998 period, simulate changes during the 1998–2014 period, and validate the simulation for the 1998–2014 period. Following an established method, this study assessed the three types of land change: (1) reference change during the calibration time interval, (2) simulation change during the validation time interval, and (3) reference change during the validation time interval, using intensity analysis and figure of merit components (hits, misses, and false alarms). The results revealed the cause of the low accuracy of the national scale land-use scenarios as well as priority solutions, such as aligning the underlying spatial vegetation maps and improving the model to reduce two types of disagreement between the simulation and reference maps. These findings should help to improve the accuracy of model predictions and help to better inform policymakers during the decision-making process.