We identified intraoceanic thrusts developed as imbricate structures within the subducting Philippine Sea plate off the Kii Peninsula in central Japan manifesting as strong-amplitude reflections observed in an industry-standard three-dimensional (3D) seismic reflection data set. These imbricate intraoceanic thrusts cut through the oceanic crust as a discontinuous thrust plane striking approximately parallel to the trench. In our survey area, large intraplate earthquakes with moment magnitudes (Mw) over 7 occurred on 5 September 2004, causing strong ground motions on the islands of Japan and tsunami waves. The locations of the intraoceanic thrusts recognized in the seismic data are distributed around the estimated hypocenters of the mainshocks and aftershocks of the 2004 earthquakes. Furthermore, their geometry extracted from the 3D seismic data could explain the kind of complex rupture pattern observed during the 2004 events. Therefore we propose that the intraoceanic thrusts are seismogenically active.