The velocity structure at the western segment of the Atotsugawa fault system is elucidated by inverting arrival times from local earthquakes and explosive sources using double-difference tomography. Bodies with high P-wave velocities (Vp) are imaged at depths greater than 2 km beneath surface traces of the Atotsugawa fault system. The high velocity bodies, which tilt gently to the south, markedly coincide with zones of high electrical resistivity. Quite low resistive zones at shallower depths in the vicinity of the fault correspond to bodies with low Vp and high Vp/Vs. The top of the high-velocity bodies is deeper in the northern and southern areas than that in the center of the fault system, showing a convex upward-shape within the Niigata-Kobe Tectonic Zone (NKTZ). Lateral variations in upper crustal structures could partially contribute to the observed large increase in compressional strain within the NKTZ.