A controller for a power conversion system reduces common-mode voltage generated by the power conversion system by imposing a constraint on the control signals applied to the power conversion system. The power conversion system includes a plurality of switching devices that are responsive to control signals provided by the controller to selectively connect each output of the power conversion system to one of a plurality of inputs. The controller generates control signals based on a desired output of the power conversion system. In addition, the controller imposes a constraint on the control signals to reduce the common-mode voltage. The constraint is defined by assigning an integer value to each input of the power conversion system, and requiring that the selective connection of outputs to inputs must result in a sum of integer values equal to zero.