The operating system is the most important software component of any computer, and therefore, the security of the enterprise information system as a whole depends on the level of implementation of the security policy in a single operating system. In general, Linux operating systems (OS) cannot be considered as a ready-to-use security system. There are many recommendations on improving Linux security, but the authors of these recommendations do not guarantee that their recommendations are sufficient to achieve the required level of system security. This study attempts to systematize available methods for increasing the level of security of application software for Linux-like OSs operating as part of control systems at nuclear power facilities. The required level of security of the entire system can be achieved at the application software level.