The Hida Mountains in central Japan are well-known as an attenuation zone for seismic waves. We estimated a three-dimensional S-wave attenuation structure beneath central Japan, including the Hida Mountains region. The \({Qs}^{-1}\) values in blocks of \({0.1}^{^\circ }\times {0.1}^{^\circ }\times 10\) km (latitude × longitude × depth) were estimated by comparing observed and theoretical spectral amplitudes in the frequency range of 1–10 Hz. We analyzed seismic records, including coda waves, and the estimated \({Qs}^{-1}\) reflects the sum of scattering and intrinsic attenuation. It was found that the upper crust beneath the Hida Mountains shows a strong attenuation for the S-wave. The upper crust beneath the Boso Peninsula attenuated the seismic wave considerably. Many of the shallow high-attenuation regions are known as high uplift rate areas. High deformation rate areas along the southern coast of central Japan due to the subduction of the Philippine Sea plate also indicated high attenuation. It was estimated that cracks in the upper crust produced by crustal deformation would be related to the high attenuation in the regions. A low-attenuation area in the lower crust was recognized beneath central Japan, where the Philippine Sea slab acts as a barrier for upwelling melt and/or fluid. A low-attenuation belt of more than 300 km in length was imaged in the lower crust. At the depth of 30–40 km, a high-attenuation area was estimated, which would be related to the volcanic chain deflected toward the back-arc side in northern central Japan. Under the Philippine Sea slab, a high-attenuation zone was recognized, which continued to the Mt. Fuji area.
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