This paper reports the automation of an effi-ciency assessment process for complex systems of information security by means of an automated system formation the basic functions of which are: carrying out of information security (IS) audit, model formation of IS threats, recommendations for the formation of information security systems, a set of organization-regulatory documentation. For the solution of a problem in the efficiency assessment of confidential information protection there is developed a simulator and a universal criterion taking into account a probability of the realization and combating threats and allowing the estimation of the complex system efficiency for information protection in dynamics of processes occurred. The approach offered to the assessment of an information security level of an information object allows reducing considerably material and time costs for carrying out information security audit and also increasing the design solutions quality at the creation and introduction of complex system of information protection.