SUMMARY During moderate to deep (35–260 km) earthquakes within the Philippine-sea slab along the Ryukyu arc, distinctive later phases after S are observed across the Japanese archipelago for epicentral distances from 1500 to 2200 km, producing anomalous amplification of ground motion in central and northern Japan. Broad-band observations show that these later phases have a faster apparent wave speed (7–9.5 km s−1) than S, and are dominant at low frequencies (0.05–1 Hz), indicating S-wave reflections returned from the upper mantle with strong attenuation for high frequencies. Numerical simulation of seismic wave propagation in 3-D models including subduction of both the Pacific (PAC) and Philippine-sea (PHS) plates reveal the origin of these reflections. The triplicated S wave front from the 410 km discontinuity undergoes wide-angle reflection at the top of the Pacific slab bringing strong amplitudes in a narrow band of epicentral distance near 1500 km. Also, wide-angle S reflections at the 660 km discontinuity are reinforced by refraction when travelling through the high-wave speed Pacific slab; these arrive at the surface beyond 2000 km epicentral distance. The characteristics of the deep mantle reflections and the distribution of large ground motion across Japan due to the reflections are strongly dependent on the source depth and distance to the Ryukyu earthquakes. Tomographic imagery for western Japan indicates loss of the high-wave speed signal of the PAC slab below 200 km depth; the character of the large S reflections and pattern of enhanced ground motions favours a model in which the PAC slab is thinned rather than fully broken. The peculiar pattern of ground motion from Ryukyu earthquakes can be useful for constraining deep slab structures that are difficult to identify based on tomography.