Roll stabilization systems for ships are employed to increase comfort for passengers, maintain full working capabilities for members of the crew and prevent cargo damage. In this paper, we have investigated the usefulness of active stabilizing system to reduce ship rolling under disturbances, using varied reaction of the flaps. In the proposed anti-rolling system for a ship, the flaps as the actuator are installed on the stern to reject rolling motion induced by disturbances such as wave. The action induced by flaps depends on power of disturbances and can take the ship balance. Especially, in this study we define the system parameters under the given system structure and design the controller to evaluate the usefulness of the proposed system.