In this investigation, we examine the uncertainties using the horizontal-to-vertical spectral ratio (HVSR) technique on earthquake recordings to detect site resonant frequencies at 207 KiK-net sites. Our results show that the scenario dependence of response (pseudospectral acceleration) spectral ratio could bias the estimates of resonant frequencies for sites having multiple significant peaks with comparable amplitudes. Thus, the Fourier amplitude spectrum (FAS) should be preferred in computing HVSR. For more than 80% of the investigated sites, the first peak (in the frequency domain) on the average HVSR curve over multiple sites coincides with the highest peak. However, for sites with multiple peaks, the highest peak frequency (f(p)) is less susceptible to the selection criteria of significant peaks and the extent of smoothing to spectrum than the first peak frequency (f(0)). Meanwhile, in comparison to the surface-to-borehole spectral ratio, f(0) tends to underestimate the predominant frequency (at which the largest amplification occurs) more than f(p). In addition, in terms of characterizing linear site response, f(p) shows a better overall performance than f(0). Based on these findings, we thus recommend that seismic network operators provide f(p) on the average HVSRFAS curve as a priority, ideally together with the average HVSRFAS curve in site characterization.