Using 136-MHz Faraday rotation data obtained at three closely spaced stations, we present evidence that severe nightime gigahertz scintillations, which appear rarely at mid-latitudes around Japan only during geomagnetic storm conditions, are closely associated with deep depletions of total electron content (TEC). The TEC depletions amount to 2--8¿1016 el/m2 (10--30% of the background TEC), and their durations range from 10 min to 1 hour. These depletions move northeastward or eastward with velocities between 60 and 260 m/s. The depletions are probably not counterparts of the equatorial bubbles but seem to be formed in localized regions around Japan under complicated and peculiar ionospheric conditions. There is an indication that the oscillation of the F region caused by large-scale TID's propagating from north to south (~600 m/s) may initiate the generation of the depletion.