The invention applies to servo controllers for at least the voice coil motor of a hard disk drive. Today, many control algorithms require 80 to 90 percent of the sampling period to complete their calculation of the next control, making computation time delay no longer negligible. The invention accommodates the transport delay, such as computation time delay, into the state estimator and into the whole control system. Experimental results using a commercial hard drive, as well as simulation results, show that the invention's method effectively improves the hard disk drive control system stability by increasing the phase margin and gain margin. The invention includes the method of operating the servo-controller, as well as the apparatus implementing that method. The invention also includes hard disk drives containing servo-controllers implementing the method, and program systems residing in accessibly coupled memory to a computer within the servo controller implementing the method.