A passive three-phase rectifier circuit equipped with a “Flying Converter Cell” (FCC) active current shaping network, based on the third harmonic injection concept, has been introduced recently. This additional/optional circuit allows the upgrade of a standard B6 diode rectifier to a low harmonic input stage with unity power factor. In order to guarantee properly shaped sinusoidal mains input currents, dedicated current and voltage controllers of the active circuitry must be designed carefully. As the active current injection unit consists of an assembly of three individual converter stages, the design procedure of both current and superimposed voltage controllers results in fairly high complexity. It is, therefore, going to be discussed in detail in this work. Based on the analysis of the rectifier system, an appropriate control concept is developed which is implemented using a digital signal processor. It is furthermore shown that the midpoint voltage of the FCC can advantageously be used for balancing of the dc capacitor stage of the cell without deteriorating total harmonic distortion of mains input currents. Measurement results taken from a 10 kW/10 kHz laboratory prototype finally confirm promising characteristics of the total hybrid system.