Following the 1995 Hyogo-ken Nanbu Kobe. Earthquake, the Japanese government, in an effort to prevent future earthquake disasters, installed networks consisting of a large number of strong-motion observation stations. Further, national seismic hazard maps were made available to the public on an Internet website in March 2005 by the Headquarters for Earthquake Research Promotion. However, these maps indicate only the local seismic intensity for Japan, as empirically converted from predicted peak velocity in consolidated soils. For various applications, other strong-motion indexes such as the response spectral acceleration are required. In this study, a database of whole Japanese strong ground motion records between 1963 and 2003 is established in order to identify a new standard attenuation relation for Japan, for response acceleration as well as peak value. It is usually very difficult to determine a suitable model form due to the large variability of strong-motion data and correlation among the model variables, because the strong coupling of variables in an attenuation model, and the statistical power of the data is often not large enough to determine the necessity of these parameters. Therefore, in this study, our model has only three variables: earthquake magnitude, shortest distance to the seismic fault plane, and focal depth. To improve predictions given by the model, site correction terms are adopted and additional terms for correcting regional anomalous seismic intensity with respect to the base model are determined. The good fit between the model and observed strong-motion records suggests that the new model is reasonably robust.