A waveform inversion with empirical Green’s functions was conducted to estimate strong-motion generation areas (SMGAs) of the 2003 Tokachi-oki, Japan, earthquake (Mw 8.3). Although the rupture process of this great subduction-zone earthquake has been revealed with waveform inversions based on low-frequency (lower than 0.2 Hz) ground motions, it is much more important from an engineering point of view to investigate how strong ground motions with higher frequencies were generated from the earthquake. Waveform data with higher frequencies have been excluded from the conventional inversions because of the difficulty in computing realistic theoretical Green’s functions at higher frequencies. In this study, with the aid of empirical Green’s functions, we extended the applicability of the waveform inversion to higher-frequency ground motions up to 1 Hz. We selected three aftershocks for use in the analysis, referring to the similarity of the group delay time between the mainshock and the aftershock records. The resultant slip model has three SMGAs, each of which is close to the hypocenter of one of the aftershocks used. Generally speaking, locations of the SMGAs identified in this study agree well with asperities identified from the inverted results using low-frequency (lower than 0.2 Hz) ground motions plus geodetic data and tsunamis. It implies that strong ground motions up to 1 Hz were generated from almost the same asperities producing lower-frequency ground motions. In terms of the complexity of slip models, although our analysis is focused on high frequencies, our slip model is at least as simple as conventional low-frequency slip models. Such results would be useful in constructing source models of future great subduction-zone earthquakes for strong-motion prediction.