We estimate the three-dimensional (3D) P-wave attenuation structure beneath the Niigata-Kobe Tectonic Zone (NKTZ), central Japan, using high-quality waveform data from a large number of stations. The obtained results confirm the segmentation of the NKTZ into three regions, as suggested by 3D seismic velocity models, and reveal characteristic structures related to surface deformation, shallow subduction of the Philippine Sea slab, and magmatism. The lower crust beneath the NKTZ west of the Itoigawa-Shizuoka Tectonic Line (ISTL) is overall characterized by distinct high attenuation, whereas the upper crust shows marked high attenuation to the east of the ISTL. Differences in the depths of anelastically weakened parts of the crust probably result in a first-order spatial variation in surface deformation, forming wide (width of ~100 km) and narrow (width of 25-40 km) deformation zones on the western and eastern sides of the ISTL, respectively. Many M ≥ 6.5 earthquakes occur in the upper crust where seismic attenuation in the underlying lower crust varies sharply, suggesting that spatial variations in rates of anelastic deformation in the lower crust result in stress concentration in the overlying brittle crust. We interpret a moderate-to low-attenuation zone located in the lower crust at the northeast of Biwa Lake to reflect low-temperature conditions that are developed locally as a result of shallow subduction of the cold Philippine Sea slab.