The growing shortage of resources has led to an increase in the uncertainties inherent in the processes of designing, producing and operating items and systems of weapons, military and special equipment (AMSE), which has exacerbated the problem of accuracy of cost forecasting in planning. The efficiency of the executives’ decisions directly depends on the established criterion of economic efficiency of the management system of an integrated industrial company (IIC). A holistic approach is based on the use of individual functional mechanisms, taking into account the laws of synergy and the definition of a synergistic effect. As part of assessing the effectiveness of IIC management systems, it is necessary to follow the principles of a rational combination of administrative and economic forms and methods of managing the departments. Optimization of management systems of IIC can be achieved by improving the system of interaction between structural units and reducing unproductive costs.