Current shipboard control systems contain significant levels of automation to perform complex functions such as navigation and propulsion control. The purpose for employing automated systems has been to reduce costs and improve performance. While automation offers great benefits, it also introduces a set of corresponding cyber security related risks. Current ships carry only limited cyber security systems. In order to advance the level of cyber security in shipboard control systems, this paper introduces novel security design methods which are designed to be embedded within the control system itself. This paper also outlines a potential method for evaluating the cyber security value of such patterns in the context of shipboard control systems.