The existence of a static fault segment boundary has been proposed for segmentation of the historical great earthquakes along the Nankai Trough, southwest of Japan. Due to the extremely low seismicity, the seismic characteristics around the boundary have remained too uncertain to allow detailed discussion of the cause of the fault segmentation. We collected four years of continuous seismic data around the segment boundary through repeated marine observations and determined accurate hypocenters, magnitudes and focal mechanisms of the observed earthquakes. The Tokai segment to the east of the boundary shows particularly low seismicity. An abrupt change in the P-axis orientation of intra-slab earthquakes coincides with heterogeneous structure within the subducting Philippine Sea Plate. The boundaries between regions of different seismic character are parallel to the magnetic anomaly lineation over the Shikoku Basin of the subducting plate, implying that they are determined by the formation process of the basin.