The technique of estimation of protection of critically important properties of the automated systems as objects of critical information infrastructure is offered. Privacy, integrity and availability of protected resources with different categories of importance are identified as critical properties. It is shown that the existing models of information security systems as part of automated systems and methods for assessing the security of critical properties do not fully reflect the specifics of information security systems as complex organizational and technical systems, the behavior of which, as a rule, reflects the dynamics of poorly structured processes, characterized by a high degree of uncertainty due to non-stationarity, inaccuracy and insufficiency of observations, fuzzy and unstable trends. The reliability of estimates of resource security of automated systems significantly depends on the selected model of formation of the structure of the information security system. Most effective way to increase the reliability of estimates of security is the distribution model of protection mechanisms in the neutralized threats. The statement and the scientific problem of estimation in the conditions of high uncertainty of protection of resources of the automated systems from violations of its critical properties-confidentiality, integrity and availability of the protected resources with various categories of importance is resulted. Determined constraints and assumptions for the task. On the basis of the model of formation of structure of information security system of automated systems by distribution of protection mechanisms on neutralizable threats of information security the values of potential risk from realization of actual threats are determined for each level of protection. The technique is used in the design and development of automated systems of state and military administration.