Autonomous systems based on the "Internet of Things" paradigm have become widespread. The Internet of Things devices are used for collecting and analyzing data, control electrical systems. The Internet of Things the most common fields of use are smart houses, smart cities, smart traffic, environment monitoring, healthcare etc. With the automation to the degree of autonomy of such processes as cargo delivery and human transportation, the Internet of Things paradigm begins to extend not only to stationary devices, but also to mobile, primarily small unmanned aerial vehicles. UAV can be used not only for civil use but for police or military operations too. This poses a potential threat to skilled criminals such as terrorists, smugglers and drug couriers. There is an urgent problem of secure transmission of data and control signals at distances up to tens of kilometers without loss of communication and the possibility of interception of control. Wireless communication technologies are widely used in all areas of the economy: control systems, environmental safety monitoring, industrial automation, logistics, etc. Wireless networks have many characteristics in common with wireline networks, and therefore, many security issues of wireline networks apply to the wireless environment. Wireless data is easy to intercept by potential eavesdroppers. Issue of security and privacy become more notable with wireless networks. The paper substantiates the transition to cryptographically protected wireless communication channels in autonomous control systems for both fixed and mobile performance. Possible attack vectors in such systems are considered. An analytical review and classification of modern cryptographic protection (encryption) algorithms used at the representative, session and channel levels of communication interfaces together and functional diagrams for some of them are performed. Selected criteria for comparing cryptographic algorithms, which allows you to choose the best depending on the functions performed and the conditions of use of a particular autonomous system.