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This paper presents a thrust loss suppression algorithm in an electric propulsion ship. From the viewpoint of the speed controller of the propulsion motor, the thrust loss due to cavitation can be regarded as a disturbance torque. The disturbance torque is estimated by means of a disturbance observer. Considering the estimated disturbance torque, the speed reference of the propeller is modified to suppress the thrust loss. The experimental results which performed in the cavitation tunnel with an electrically driven propulsion system are shown to verify the proposed algorithm.