We conducted centroid moment tensor inversions of shallow very low frequency earthquakes (SVLFEs) that occurred around off the southeast Kii Peninsula, Japan. A set of Green's functions was evaluated using numerical simulations of seismic wave propagation in a three‐dimensional velocity structure model, including the subducting Philippine Sea slab and the accretionary prism. We used observed seismograms for periods of 20–50 s at an onshore broadband network, which enable us to investigate the long‐term activity of SVLFEs. Estimated centroid locations and focal mechanisms of SVLFEs, including SVLFEs that occurred prior to the deployment of seafloor observations, were very similar to those estimated using seafloor records. Low‐angle thrust faulting mechanisms were concentrated around the accretionary prism toe. SVLFE activity in April 2016 was concentrated further west in an area of previous activity. Our results imply seismic slip around the very shallow part of the Philippine Sea plate boundary.