The article considers a complex problem of providing confidence in the used control systems of technological equipment, developed in Russia in conditions of technological backwardness and high dependence on imports of complete control systems, their components and software. A methodology for the system representation of confidence in technological equipment control systems, based on the description of confidence in the system comprising confidence in its constituent quasi-autonomous elements, is investigated. The authors disclose a sequence of quantitative assessment of confidence, determined from the confidence in the results of the development and testing of control systems, their components and software from the viewpoint of functional reliability and information security. Possibilities of increasing confidence in control systems are considered, and the problem of providing functional reliability and information security is analyzed. As part of the study of the problem of information security of control systems of technological equipment, threats associated with vulnerabilities and malware are considered. In addition, the study systematizes undocumented features and considers methods for their detection.