A low-velocity zone (LVZ) has been detected by seismic exploration surveys within the Nankai accretionary prism toe off the Kii Peninsula, southwestern Japan, and is considered to be a mechanically weak volume at depth. Such mechanical heterogeneities potentially influence seismic and tsunamigenic slips on megathrust earthquakes in the subduction zone. However, the spatial distribution of the LVZ along the trough-parallel direction is still elusive. Here we show sporadic LVZs in the prism toe from one-dimensional shear wave velocity (Vs) profiles obtained at 49 cabled ocean bottom stations, which were estimated by a nonlinear inversion technique, simulated annealing, using the displacement-pressure ratios of the Rayleigh wave. The estimated distribution of LVZs along the trough widely correlates with the epicentres of shallow very low frequency earthquakes (sVLFEs), which suggests that sVLFEs are activated in the sporadically distributed low-velocity and mechanically weak volumes where fluids significantly reduce the shear strength of faults.