In seagoing ships in waves, the torque and thrust of the propeller may vary with the submergence depth of the propeller. A large ship motion can cause ventilation and loss of effective disc area, which degrade the ship's propulsion efficiency. Electric or electrified ships powered by electric motors can respond quickly to such load variations, unlike conventional ships powered by internal combustion engines. This paper proposes a model predictive anti-spin thruster control algorithm that can improve the propulsion efficiency of electric ships by controlling the rotational speed of the propeller with consideration of time-varying load conditions. The weight of the cost function for optimizing the propulsion efficiency is adjusted by using the propeller's submergence predicted by an autoregressive model. The feasibility of the proposed algorithm is shown through numerical simulations of ship motions and propeller depth variation in irregular waves. The performance of the proposed algorithm is validated and compared with that of shaft speed and anti-spin thruster controllers, and the results are discussed.