We investigated the effects of the propagation path and site amplification of shallow tremors along the Nankai Trough. Using far-field S-wave propagation from intraslab earthquake data, the amplification factors at the DONET stations were 5–40 times against an inland outcrop rock site. Thick (~5 km) sedimentary layers with VS of 0.6–2 km/s beneath DONET stations have been confirmed by seismological studies. To investigate the effects of thick sedimentary layers, we synthesized seismograms of shallow tremors and intraslab earthquakes at seafloor stations. The ratios of the maximum amplitudes from the synthetic intraslab seismograms between models with and without thick sedimentary layers were 1–2. This means that the estimated large amplifications are primarily controlled by thin lower-velocity (< 0.6 km/s) sediments just below the stations. Conversely, at near-source (≤ 20 km) distances, 1-order amplifications of seismic energies for a shallow tremor source can occur due to thick sedimentary layers. Multiple S-wave reflections between the seafloor and plate interface are contaminated in tremor envelopes; consequently, seismic energy and duration are overestimated. If a shallow tremor occurs within underthrust sediments, the overestimation becomes stronger because of the invalid rigidity assumptions around the source region. After 1-order corrections of seismic energies of shallow tremors along the Nankai Trough, the scaled energies of seismic slow earthquakes were 10-10–10-9 irrespective of the region and source depth. Hence, the physical mechanisms governing seismic slow earthquakes can be the same, irrespective of the region and source depth.