Abstract Earlier the model studies demonstrated that equatorial F2 layer stratification and an additional F3 layer appear in simulation results only by taking into account zonal electric field. Nanan Balan concluded that F3 layer forms during morning–noon period, when the ionization processes dominate over chemical losses and when there is a large upward flow of ionization due to the combined effect of E×B drift and neutral wind. Our recent studies specify that during geomagnetic storms, a non-uniform in height zonal electric fields at the geomagnetic equator form the additional layers above regular F2 layer. In this paper, we consider the formation mechanism of the additional layers in a near-equatorial ionosphere during quiet geomagnetic conditions. This study presents the comparison of the GSM TIP numerical simulations and observation data of Intercosmos-19 satellite. We confirmed that the non-uniform in height vertical plasma drifts form the additional layers at the geomagnetic equator.