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This paper uses a novel approach for the control of three-level neutral-point-clamped (NPC) rectifiers in order to tackle the capacitor voltage balance problem. A distinctive feature of the new control approach is that it is based on a model which is written in terms of the duty ratios for each phase at each level. Hence, the system model presents nine duty cycle variables. Despite the fact that this formulation is different from the usual ones, it is shown that the control problem of currents and dc-link voltage can be formulated in a similar way to conventional methods. Furthermore, the control of the capacitor voltage balance can be expressed by means of equations that are decoupled from the currents and dc-link voltage dynamics, which results in a specific controller for the voltage balancing that does not affect the previous dynamics. A key point of the proposed approach is that part of the modulation stage is implicit in the formulation. Two particular controllers are compared in this paper. The first one fulfills the different control objectives at the expense of a large number of commutations. This problem is overcome in a new proposed controller, which presents similar performance and a satisfactory number of commutations. Experimental results are performed showing the effectiveness compared with a modified virtual space vector modulation with capacitor voltage balance capabilities.