This paper addresses motion control issues of flexible joint robot manipulators using joint torque feedback. A two-stage control scheme consisting of a motion controller and a joint torque controller is established in a systematic way for the general n-link case. To deal with uncertainties in the robotic system, a robust adaptive control algorithm is developed assuming that all system parameters including the joint flexibility values are unknown except for some of their bounds. The system stability is analyzed via Lyapunov stability theory. The result has the distinct feature that no restriction of joint flexibility, nor exact knowledge of the parameters of rotor subsystem is required. The outcome is a useful framework for generalization of control methods previously developed for rigid robots. Simulation results verify the effectiveness of the proposed control methods.