Low-frequency earthquakes (LFEs) are categorized as slow earthquakes whose spectral power is concentrated at 1–4 Hz. While the tectonic LFEs along megathrust boundaries occur as shear failure, LFE generation in the continental plate, which is widespread in the lower crust and rarely occurs in the brittle upper crust, is poorly understood due to the diversity of focal mechanism solutions. Here we conduct a systematic survey of LFEs using two metrics (frequency index and peak frequency) that characterize the frequency content of the waveforms, and show that LFEs are prevalent in the upper crust beneath the Japanese Islands, even in non-volcanic regions. Shallow LFEs are most common near tectonic boundaries, and are temporarily activated in the aftershock sequences of large (M³6.5) crustal earthquakes. The widespread distribution of shallow LFEs suggests that a lower crustal rheology is not necessary for their genesis. We infer that failure along frictionally weakened faults due to high pore-fluid pressures is a primary control for the enrichment of low-frequency energy. The observed differences in the frequency content are probably due to differences in the pore-fluid pressure along each fault, which influences the rupture velocity and magnitude of the tensile component during shear failure. Our observations may lead to a more unified model of earthquake generation, thereby providing a better understanding of how earthquakes release the stress accumulated in the Earth.