The paper addresses principles and methods of protection design of control systems (CS) of critical facilities (CF) from damage factors of technogenic accidents and catastrophes. It is necessary to note that when assessing the protectability level of СF control systems one should take into consideration mechanical, thermal, electromagnetic, radiation and other effects. The basic kinds of vulnerabilities of CS are identifi ed. These include: objective, subjective and stochastic vulnerabilities. The paper presents an algorithm for protection design of a control system based on threat and vulnerability analysis, the main directions of vulnerability reduction for control systems are discussed. The protection schemes based on classical concept of in-depth defense for protecting CF control systems are introduced.