A fault detection system for an over-speed protection system of a rotating machine includes a first speed sensor, second speed sensor, and third speed sensor sensing a speed of a shaft of the rotating machine. The system includes a first input configured to receive a first pulse train from the first speed sensor, a second input configured to receive a second pulse train from the second speed sensor, a third input configured to receive a third pulse train from the third speed sensor, and a processor configured to generate a shutdown signal for the rotating machine based on the first pulse train, the second pulse train, and the third pulse train.