The three-dimensional (3D) S-wave attenuation (Qs) structure beneath the Kanto plain, where the Pacific and Philippine Sea plates subduct, was estimated using strong-motion records of the K-NET and KiK-net. In addition to several low-Qs zones corresponding to the volcanic front, a large NW--SE trending low-Qs zone is estimated under the non-volcanic Kanto area at depths of 20--60 km. This zone corresponds to a previously identified low-velocity (both Vp and Vs) zone with a high Poisson's ratio at 40-km depth; it further indicates a wedge immediately above the subducting Philippine Sea plate. Predicted seismic ground motions using the estimated 3D attenuation structure is very similar to the actually recorded by recent earthquake on July 2005 (M = 6).