Recent studies of slow earthquakes along plate boundaries have shown that tectonic tremor, low-frequency earthquakes, very-low-frequency events (VLFEs), and slow-slip events (SSEs) often accompany each other and appear to share common source faults. However, the source processes of slow events occurring in the shallow part of plate boundaries are not well known because seismic observations have been limited to land-based stations, which offer poor resolution beneath offshore plate boundaries. Here we use data obtained from seafloor observation networks in the Nankai trough, southwest of Japan, to investigate shallow VLFEs in detail. Coincident with the VLFE activity, signals indicative of shallow SSEs were detected by geodetic observations at seafloor borehole observatories in the same region. We find that the shallow VLFEs and SSEs share common source regions and almost identical time histories of moment release. We conclude that these slow events arise from the same fault slip and that VLFEs represent relatively high-frequency fluctuations of slip during SSEs.