The financial system of a modern state is a complex interconnected structure. Ensuring the correct functioning of all its elements requires special organizational and control measures at all levels of government. At the same time, changes in the economic and political situation require flexibility from the system, which, in the case of the size of the Russian Federation, imposes the need to create mechanisms for operational and sufficient control and influence. A significant part of the mechanisms for providing the necessary properties of the regulatory framework is laid down in the documents of methodological support. The article is devoted to solving the main problems and developing recommendations for improving the procedures for improving the quality of audit of the effectiveness of the use of budgetary funds. The study is conducted on the basis of published audit reports. An additional tool for studying information about existing problems is the regularly published Bulletin of the Accounts Chamber of the Russian Federation. The subject of attention in the case of studying open documents is not so much the essence described in the relevant section, but the content itself and the approach to covering the issue under study. The conducted research examines the list of issues on methodological support of the relevant procedures for conducting an efficiency audit both in a broad sense and in an appendix directly to the topic of this article, taking into account the political, economic and other factors relevant at the time of control and expert-analytical activities. The final part is devoted to the most pressing problems identified during the study period and ways to both reduce their negative impact on the existing system and ways to eliminate them as classes.