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A comprehensive dynamic model of the three-level Neutral Point Diode Clamped (NPC) converter, based on the generalized state-space averaging method, is presented. The developed model mathematically describes (i) the reason for and (ii) the impacts of the system parameter tolerances on the drift/imbalance of the DC-side capacitor voltages. Then, based on the developed model (i) a novel controller to prevent DC capacitor voltage drift/imbalance and (ii) a decoupled current controller in the dq-frame are designed. The paper also presents a feed-forward control to eliminate the coupling between the voltage balancer and the current controller. The accuracy of developed NPC converter model and the effectiveness of the proposed controls are verified by time-domain simulations of a study system in the PSCAD/EMTDC environment.