A gas turbine engine control system is disclosed having a fault detection system capable of detecting a high N1 condition. N1 rotational speed is measured and, in two different locations, subtracted from a target N1 value and a requested N1 value. The resultant error values are scaled by a gain that is scheduled as a function of N2 rotational rate. Each error value is accumulated with separate integrators that have independent maximum and minimum limits. The integrators are reset based upon a number of conditions. A number of additional conditions must also be satisfied for the fault detection system to trigger a fault condition. If the additional conditions are satisfied and the integrators are accumulating values, then a fault condition is set if either or both integrators accumulate a value that reaches a selected limit.