In one embodiment, a magnetic disk apparatus comprises a magnetic disk for recording information; a magnetic head that reads information from, or writes information to, the magnetic disk; an actuator device that drives the magnetic head; and a control system that controls the driving of the actuator device. The actuator device is configured by a dual stage actuator comprising a fine actuator that drives the head and a coarse actuator that drives the magnetic head together with the fine actuator. The control system includes a fine controller that generates an operational value for driving the fine actuator and a coarse controller that generates an operational amount for driving the coarse actuator. The control system includes a mechanism for smoothly changing the operational amount generated by the fine controller immediately before saturation resulting from an applied voltage limit of the fine actuator or at the time the fine actuator returns to a control range from the saturation.