A fault protection system provides fault protection to a permanent magnet (PM) generator. The fault protection system includes one or more overload and short-circuit protection circuits, an unbalanced protection circuit and a thermal protection circuit. The overload and short-circuit protection circuit detects both overload and short-circuit conditions by monitoring current and voltage generated at a single phase by the PM generator. The unbalanced protection circuit monitors and compares current and voltage generated associated with at least two individual phases to determine unbalanced conditions between the phases. The thermal protection circuit detects a thermal overload condition by monitoring the temperature of the PM generator. If the overload and short circuit protection circuit, the unbalanced protection circuit, or the thermal protection circuit detects a fault signal, a control circuit causes a control device to reduce or prevent mechanical power from being supplied to the PM generator, preventing the PM generator from generating power and protecting it from damage.