In this paper, we address the design of an autopilot for autonomous landing of a helicopter on a rocking ship, due to rough sea. The deck is modeled to have a sinusoidal motion. The goal of the helicopter is to land on it during motion. In this work, we use a tether to help in target tracking. Based on the measurement of the angle between the cable and the helicopter/ship, a novel hierarchical two time-scale controller has been proposed to ensure landing of the helicopter on the ship. The system is demonstrated by computer simulation. Currently, work is under progress to implement the algorithm using an instrumented model of a helicopter using a tether.