SUMMARY We studied the scattering properties of high-frequency seismic waves due to the distribution of small-scale velocity fluctuations in the crust and upper mantle beneath Japan based on an analysis of three-component short-period seismograms and comparison with finite difference method (FDM) simulation of seismic wave propagation using various stochastic random velocity fluctuation models. Using a large number of dense High-Sensitivity Seismograph network waveform data of 310 shallow crustal earthquakes, we examined the P-wave energy partition of transverse component (PEPT), which is caused by scattering of the seismic wave in heterogeneous structure, as a function of frequency and hypocentral distances. At distance of less than D = 150km, the PEPT increases with increasing frequency and is approximately constant in the range of from D = 50 to 150 km. The PEPT was found to increase suddenly at a distance of over D = 150 km and was larger in the high-frequency band (f > 4 Hz). Therefore, strong scattering of P wave may occur around the propagation path (upper crust, lower crust andaroundMohodiscontinuity)oftheP-wavefirstarrivalphaseatdistancesoflargerthanD = 150km.WealsofoundaregionaldifferenceinthePEPT value,wherebythePEPT valueislarge at the backarc side of northeastern Japan compared with southwestern Japan and the forearc side of northeastern Japan. These PEPT results, which were derived from shallow earthquakes, indicate that the shallow structure of heterogeneity at the backarc side of northeastern Japan is stronger and more complex compared with other areas. These hypotheses, that is, the depth andregionalchangeofsmall-scalevelocityfluctuations,areexaminedby3-DFDMsimulation using various heterogeneous structure models. By comparing the observed feature of the PEPT with simulation results, we found that strong seismic wave scattering occurs in the lower crust due to relatively higher velocity and stronger heterogeneities compared with that in the upper crust. To explain the observed regional difference, the velocity fluctuation model with 3‐4 per cent stronger fluctuation and smaller κ is required at the backarc side of northeastern Japan.