During the anti-terrorist operation there is a search for appropriate ways to create and improve a scientifically sound, economically feasible system of protection of information resources in information and telecommunications networks for special purposes. This work is devoted to the consideration of methodological bases for assessing the security control of information and telecommunication networks for special purposes. The aim of the article is to increase the security of information and telecommunication networks for special purposes by using as a basic method of analysis of hierarchies and the apparatus of neural fuzzy networks to assess the security of networks of this class. The generalized characteristic of the basic groups of methods of an estimation of control of protection of information and telecommunication networks of this class is resulted. At p stopping the task of assessing the security control of information and telecommunications networks for special purposes as a system of information resources, its following indicators are determined: the priority of protected information, the probability of hacking, the cost of the protection system, system performance. To set the proposed parameters for assessing the security of the system can be used research methods that include theories: graphs, decision support systems, fuzzy sets, neural networks, methods of multicriteria optimization, expert methods. It is proposed to use as a basic method of analysis of hierarchies and apparatus of neural-fuzzy networks for further development of the method of assessment of security control of information and telecommunication network of special purpose.