In modern ship monitoring and control systems new computer technologies are applied, starting from the navigation system, communication equipment, propulsion system, cargo handling system to the auxiliary systems such as air conditioning and ventilation, fuel system, auxiliary cooling system. In spite of all the technical advances and sophisticated marine systems, the safety on a modern ship is still disputable having in mind that marine accidents occur quite frequently. Safety of navigation, among other things, depends on the safety of the ship computer system. Consequently, security of the computer systems in the context of safety at sea requires some serious consideration. This paper examines procedure of conducting penetration testing using Black box method. Short analisys of computer security gives introduction to conducting testing procedure throught 4 phases. Using free tools and software solution enviroments for pentesting, content points on easy-to-get applications and possible security breaches. Implementing processing methods, the paper analyses potential vulnerabilities and gives a practical explanation for their removal. In addition, all processes are implemented in real enviroment aiming to give clear presentation to the reader.