A harmonic drive is a compact, light-weight and high-ratio torque transmission device which is used in many electrically actuated robot manipulators. In many robotic control strategies it is assumed that the actuator is an ideal torque source. However, converting harmonic drive systems to ideal torque sources is still a challenging control problem for researchers. In this paper the torque control of harmonic drive system under free motion is examined in detail. A built-in torque sensor is developed in order to measure the torque, and by employing a Kalman filter the undesired torque signatures like torque ripples and misalignment torque are filtered out. An empirical nominal model for the system is obtained through experimental frequency response estimates, and the deviation of the system from the model is encapsulated by multiplicative uncertainty. A robust torque controller is subsequently designed in an H∞-framework and implemented employing Kalman filtered torque estimates. From time and frequency domain experiments, it is shown that the closed-loop system retains robust stability, while improving the tracking performance exceptionally well