This paper presents the thrust loss suppression algorithm in the electric propulsion ship. The thrust loss due to cavitation can be regarded as the disturbance torque. The disturbance torque is estimated by means of the 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 electric machine operating system and its controller will be shown to verify the proposed algorithm.