We have estimated broadband (f=0.5–8 Hz) site amplification factors at 1800 sites in Japan based on the coda normalization method using 4001 seismograms obtained from 48 events. The results show that, in the low‐frequency band (f=0.5–1 Hz), the site amplification factor varies over a wide range from −4 to 24 dB, with larger site amplification factors (>8 dB) in such major basins as Kushiro, Rumoi, Sapporo, Aomori, Sendai, Niigata, Tokyo, Toyama, Nagoya, Osaka, Oita, and Kagoshima. On the other hand, the site amplification factor in the high‐frequency band (f=4–8 Hz) varies over a relatively narrow range from 0 to 18 dB at each station and has no clear correlation with the surface geology of each station. We then examined the contribution of the site amplification at each station to the anomalous distribution of the intensity pattern during large earthquakes by correcting the observed ground accelerations at each K‐NET and KiK‐net station with their corresponding estimated site amplification factors. The corrected pattern of intensity shows simple concentric isoseismal intensity contours around the hypocenter, indicating the applicability of our estimates to strong motion predictions. We confirmed that our estimates are superior to those derived from geology, such as those based on the regression of the averaged S‐wave velocity from the surface to a depth of 30 m (), with a smaller standard deviation of intensity variations based on a standard decay function of intensity versus hypocentral distance.