In accordance with the general rule established by the legislation on state control and antitrust legislation, the implementation of control powers by state and municipal institutions (state-financed organizations) is not allowed. However, despite the prohibitions, other federal laws and laws of subjects of the Russian Federation provide for the possibility of certain types of control (supervision) by institutions (state-financed organizations). In some cases, institutions are endowed with supervisory powers by bodies of executive power regulations. The study identified 6 types of audits exercised by federal institutions (state-financed organizations), 5 types of control (supervision), exercised by institutions of the RF subjects and 4 types of municipal control exercised by the municipal institutions (municipality-financed organizations). The article deals with the disadvantages of control by state and municipal agencies, as well as different options for solving this problem.