The three-dimensional (3-D) P-wave velocity structure beneath Central Japan has been investigated in detail by an inversion method. 7490 P-wave arrival times from 120 shallow and intermediate depth earthquakes that have occurred in this region are used to estimate velocity anomalies in 3-D subdivided blocks and hypocentral perturbations, simultaneously. The results reveal complex 3-D structures, with low-velocity zones in the wedge portion of the upper mantle above the high-velocity Philippine Sea and Pacific plates subducting beneath this region. Prominent low-velocity bodies exist just beneath active volcanoes, particularly in the Hida mountain range. Low-velocity bodies are spatially correlated with the low- Q zones estimated from seismic intensity data. One low-velocity body coincides with an anisotropic body detected from the study of shear-wave splitting. Dome-shaped low-velocity masses seem to represent partially melted mantle diapirs. No clear evidence on velocity contrast has been identified across the Fossa Magna, which is a tectonic boundary between Northeast and Southwest Japan.