One of the most critical problems in all practical systems is the presence of uncertainties, internal and external disturbances, as well as disturbing noise, which makes the control of the system a challenging task. Another challenge with the physical systems is the possibility of cyber-attacks that the system’s cyber security against them is a critical issue. The systems related to oil and gas industries may also be subjected to cyber-attacks. The subsets of these industries can be mentioned to the oil and gas transmission industry, where ships have a critical role. This paper uses the Quantitative Feedback Theory (QFT) method to design a robust controller for the ship course system, aiming towards desired trajectory tracking. The proposed controller is robust against all uncertainties, internal and external disturbances, noise, and various possible Deception, Stealth, and Denial-of-Service (DOS) attacks. The robust controller for the ship system is designed using the QFT method and the QFTCT toolbox in MATLAB software. Numerical simulations are performed in MATLAB/Simulink for two case studies with disturbances and attacks involving intermittent sinusoidal and random behavior to demonstrate the proposed controller.