A method is disclosed for identifying wedge time shift zones on a magnetic disk of a disk drive. The disk drive further includes a spindle motor for rotating the disk at an operating speed in response to a spindle control current generated by a spindle control system, and a head that is actuated over the disk. During operation, the control systems causes a seek of the head across the disk and measures wedge-to-wedge times between servo wedges. The control system then calculates a wedge-to-wedge time shift value using the wedge-to-wedge times and determines whether the wedge-to-wedge time shift time value exceeds a predetermined threshold. If the wedge-to-wedge time shift value exceeds the predetermined threshold, then the control system identifies a wedge time shift zone, and stores information for compensating for the identified wedge time shift zone during disk operations.