Mount Fuji is the focus of intense study because of its potential hazard signaled by seismic, geologic and historical activity. Based on extensive seismic data recorded in the vicinity of Mt Fuji, coda quality factor (Q−1C) using a single scattering model hypothesis, and intrinsic and scattering quality factor (Q−1i and Q−1S) using the Multiple Lapse Time Window (MLTW) method were measured. To focus the study on the magmatic structure below Mt Fuji, the data were separated into two groups: a near-Fuji region of rays traversing an area with radius 5 km around the summit (R < 5 km), and a far-Fuji region of rays beyond a radius of 20 km around the summit (R > 20 km). This classification shows the largest discrepancy of Q−1C at a range of sampling volumes corresponding to overlapped sampling depth of about 80 km. Further, the spatial division shows significant difference of Q−1i and Q−1s at hypocentral distance of 80 km. The large difference of Q−1s in bandwidths 2–4, and 4–8 Hz indicates lithospheric heterogeneity beneath Mt Fuji with a characteristic heterogeneity scale length of about 1 km. The results have a small error range due to the large data sample, showing that all Q−1 values in the near-Fuji area are greater than those of the far-Fuji area, and Q−1i for both the near and far-Fuji areas is higher than Q−1s at high frequencies. The Q−1i and Q−1s values for far-Fuji are in the range of values for typical non-volcanic areas. The Q−1i values of the near-Fuji area are lower than those of other volcanic areas considered, where as values of Q−1s are not. The low Q−1i for the volcanic region of near-Fuji suggests that the magmatic activity, indicated by percent partial melt, in the vicinity of Mt Fuji is not as active as hot spot volcanoes, such as Kilauea, Hawaii.