A new auto-tuning algorithm for motor velocity control is presented to adjust the parameters in the feedforward and feedback PI controllers, according to identified physical parameters such as a motor time constant, viscous friction terms proportional to motor velocity and squared velocity, and Coulomb friction. The physical parameters are identified by the proposed adaptive algorithm which appropriately set up a reference model and use its state variables to adjust the feedforward controller parameters. The proposed scheme is robust to disturbance torque, compared to ordinary closed-loop identification using the motor output directly. Its effectiveness is investigated in velocity control experiment using an AC synchronous servo motor.