A control system and methods for a multilevel power converter are provided. The converter includes a rectifier coupled to a DC link having a midpoint coupled to electrical ground that divides the DC link into two halves. The control system is configured to generate a reference current command for controlling an output of the rectifier, the reference current command generated based on a difference between a desired and measured DC link voltage value. The system is also configured to determine a zero-sequence current component of input current supplied to the multilevel power converter, wherein the zero-sequence current component is associated with non-linearities in said multilevel power converter that cause ground current injection into the input current by the rectifier. The system is further configured to subtract the determined zero-sequence current component from the reference current command to reduce the ground current injected into the input current by the rectifier.