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This paper presents a tracking filter with ship’s motion compensation for a ship-borne radar tracking system. The ships maneuver is described by displacement and rotational motions in the ship-centered east-north frame. The first order Taylor series approximation of the measurement error covariance of the converted measurement is derived in the ship-centered east-north frame. The ships maneuver is compensated by incorporating the measurement error covariance of the converted measurement and displacement of the position state in the tracking filter. The simulation results via 500 Monte-Carlo runs show that the proposed method follows the target successfully and provides consistent tracking performance during ships maneuvers while the conventional tracking filter without ship motion compensation fails to track during such periods.