A new control strategy based on the singular perturbation method and integral manifold concept is introduced for flexible-joint manipulators with joint friction. In controllers so far developed based on the singular perturbation theory, the dynamics of actuators of flexible-joint manipulators are partially modelled, and the coupling between actuators and links is ignored. This assumption leads to inaccuracy in control performance and error in trajectory tracking which is crucial in high-precision manipulation tasks. In this paper, a comprehensive dynamic model which takes into account the coupling between actuators and links is developed and a composite controller is then designed based on the singular perturbation theorem and integral manifold concept. To overcome the joint friction, a novel method is introduced in which a linear feed-forward torque is designed using the principle of work and energy. Finally, the experimental set-up of a single rigid-link flexible-joint manipulator in the Robotics Laboratory at the University of Saskatchewan is used to verify the proposed controller. Experimental results employing the new controller show that the trajectory tracking error during and at the end of the motion of the robot manipulator is significantly reduced.