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The purpose of this work was to study bias error in acceleration-based transfer alignment, which is probably caused by cross-correlation between the dynamic lever-arm and the linear motion of a ship. A new prediction model for the cross-correlation-caused error is proposed in this paper. We adopt the Bernoulli-Euler Beam as a simplified ship hull-girder model to verify the existence of the cross-correlation. Then, the mathematical mechanism and the prediction model of the bias error are deduced via the ordinary least squares theory. Three factors influence the bias error in the prediction model: the amplitude of the dynamic lever arm acceleration, the amplitude of the ship motion acceleration, and the cross-correlation between them. Simulation experiments are then conducted to test the influence of the factors. The results show that the mechanism analysis is reasonable, and the bias error prediction model is in agreement with the experimental results. Thus, the proposed prediction model has the potential to deduce the bias error in high-accuracy transfer alignment. [ABSTRACT FROM AUTHOR]