Long-term predictions of geological and tectonic disturbances are key issues for the safety assessment of radioactive waste disposal, especially on the Japanese Islands. Geological predictions of disturbances should be performed by extrapolating uniform mode and rate of crustal movements under the current framework. Multiple lines of geological evidence in Japan strongly suggest that the present mode of tectonics began during the late Pliocene to early Quaternary, and was fully developed by the middle Pleistocene. The uplift rates of mountains in Japan are determined to have been approximately constant until the middle Pleistocene based on simulations of temporal changes in mean altitude developed under concurrent tectonics and denudation processes. The onset of the neotectonic mode of deformation was probably triggered by the initiation of the eastward movement of the Amur Plate and the collision of the Izu block with central Honshu. The uncertainty of predictions beyond steady-state crustal deformation would, in general, increase for long-term predictions using the extrapolation procedure. Consequently, future geological and tectonic disturbances in Japan can be estimated with relatively high reliability for the next 100,000 years.