In case of the decision of the task of design of automated control systems for crucial objects, a minimum possible level of risks at uncontrollable interference in the processes of functioning of these systems, and also minimization of negative consequences from a similar interference in the course of its operation are required. In connection with this, on the basis of the system theory of conflict management and the matrix approach to the description of the structure of complex organizational systems, the authors solved the measurement problem of establishing a correspondence between the physical properties of the object and the characteristics of its mathematical model with the aim of diagnosing the health of actuators and detecting internal conflicts between them. In this article we propose an algorithm that allows one to solve private probabilistic and statistical measurement to identify conflicts in the operation of systems of this class, both at the stage of their development and in the course of operation. In addition, the paper proposed a set of dynamic and statistical models solving private measuring tasks in the process of diagnostic decisions making on the health component of the Executive device in the automated control system. The process of diagnostic solutions making is described by a Petri net and Markov and allows one to propose a methodology to determine the functionality of the diagnostic solutions, to clarify the level of operability of the actuation mechanisms and to receive the diagnostic inference as well as to estimate operability risks of the actuation mechanisms taking into account risk factors and operability of the actuation mechanisms components. The list of the associated failure of an automated control system is also offered. The program or hardware implementation of this algorithm will allow one to create a universal remedy for diagnosing and monitoring of the automated control system integrity.