For the efficient implementation of functions in the sphere of internal control depending on the activity scale and nature, organizations create services of internal control, internal audit, risk management, and economic security; however, the functionality of these structures are not clearly defined. The main goal of this study is the allocation of responsibilities for making and implementing the decisions in the sphere of internal control, which ensures the concurrence and effectiveness of implemented measures at simultaneous nonduplication of functions. The paper deals with the study of the internal control system of an economic entity. The study determined the functional interrelation between the level of the internal control system maturity and the organizational structure of an economic entity. The author considered the structure of control authorities and their functionality based on the maturity level of the economic entity’s internal control system. The paper presents the diagrams of the feed-forward and feed-back mechanism peculiar to the full-functional internal control. Based on the generalization of theoretical provisions, the author determined the role of the internal control services as an instrument for ensuring the state of economic security of an organization. The proposed mechanism of functioning of structural divisions involved in the internal control system promotes the improvement of business management efficiency and reduces the negative impact of the external and internal factors. While developing an economic entity, the internal control system should be reconsidered, taking into account the formation of a single methodological foundation for all divisions. As a result of the study, the author recommends regularly examining (at least once a year) the divisions’ functions within the internal control system using the procedure described in the study.