Equatorial F region plasma drift velocities measured by a digital ionosonde (CADI) that was recently installed in Fortaleza, Brazil, are used to investigate magnetospheric disturbance effects in the vertical (zonal) and zonal (vertical) velocities (electric fields). For the first time we report evidence of large fluctuations in irregularity zonal drift velocities (~50--180 m/s) associated with magnetospheric disturbances. The fluctuations in the zonal velocity, anti correlated with those in vertical velocity, are unlikely to be produced by prompt penetration of disturbance meridional electric field of high latitude/magnetospheric origin. A mechanism is proposed to explain the velocity fluctuations that involves: (1) Hall polarization vertical electric field in the E-layer that is field line mapped on to F-layer, and (2) electric field caused by vertical current arising from divergence in field line integrated zonal Pedersen current; both produced by the primary disturbance zonal electric field. Enhanced nighttime E region conductivity with possible spatial gradients, a requirement for the functioning of this mechanism, is observed to be present from other simultaneous measurements, whose source is suggested to be particle induced ionization in the south Atlantic Magnetic Anomaly (SAMA) zone, as known also from previous studies. ¿ 1998 American Geophysical Union