A controller for a rotary machine includes a processor and a memory coupled to the processor. The memory is configured to store operating modes of the controller. The operating modes include a normal operating mode and a fault tolerant operating mode. The controller is configured to receive a signal from at least one sensor and determine an operating state of the rotary machine based on the signal. The controller is also configured to switch the operating modes based on the determined operating state of the rotary machine and regulate at least one electromagnetic bearing and at least one flow control device. The controller is further configured to adjust at least one of the at least one electromagnetic bearing and the at least one flow control device in the fault tolerant operating mode.