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In this paper, we address the design of an autopilot for autonomous landing of a helicopter on a rocking ship, due to rough sea. A tether is used for landing and securing a helicopter to the deck of the ship in rough weather. A detailed nonlinear dynamic model for the helicopter is used. This model is underactuated, where the rotational motion couples into the translation. This property is used to design controllers which separate the time scales of rotation and translation. It is shown that the tether tension can be used to couple the translation of the helicopter to the rotation. Two controllers are proposed in this paper. In the first, the rotation time scale is chosen much shorter than the translation, and the rotation reference signals are created to achieve a desired controlled behavior of the translation. In the second, due to coupling of the translation of the helicopter to the rotation through the tether, the translation reference rates are created to achieve a desired controlled behavior of the attitude and altitude. Controller A is proposed for use when the helicopter is far away from the goal, while Controller B is for the case when the helicopter is close to the ship. The proposed control schemes are proved to be robust to the tracking error of its internal loop and results in local exponential stability. The performance of the control system is demonstrated by computer simulations. Currently, work is in progress to implement the algorithm using an instrumented model of a helicopter with a tether.