A family of core-reflected shear waves generated by the 28 June 2002 Vladivostok deep earthquake, including near vertical reflections from the 410- and 660-km discontinuities, were recorded by ~500 tiltmeters of the Hi-net and ~60 broadband seismometers of the F-net in Japan. The observed upper mantle reflections were cross-correlated with synthetics calculated on the basis of the spectral element method for a fully three-dimensional Earth model using the Earth Simulator supercomputer to accurately determine the depths of the reflection points. The mapped upper mantle discontinuities were compared with a high-resolution P wave tomographic image. The 660-km discontinuity is depressed at a constant level of ~15 km along the bottom of the horizontally extending aseismic slab under southwestern Japan. The transition from the normal to the depressed level occurs within a lateral distance of less than ~200 km. Observations suggest that the reflections from the 410-km discontinuity interfere with those from slab-related structures on top of this discontinuity, leading to a spuriously large elevation of the 410-km discontinuity in and near the subducted slab. Records at stations relatively free from such interference effects, however, still imply elevation of this discontinuity within the slab.