The need to take into account imbalances among regional indicators in the development of state policy for financing national projects makes it necessary to develop a methodology that will enable objective assessment of the effectiveness of socially significant projects in Russia. This paper reports the development of a methodology for financial monitoring of national project implementations in the constituent entities of the Russian Federation, taking into account the correlation of their target indicators and using cluster analysis and methods in mathematical statistics. The proposed methodology was tested on health and demography national project data obtained from the Federal Treasury of Russia, the Federal State Statistics Service and the Accounts Chamber for 2020–2021. The analysis of public funding for national projects based on centralization indices and target indicators for their implementation enabled classifying the regions of Russia according to the levels of effectiveness and the financial risks of implementing the projects. The results of the study correspond to the actual effectiveness of national projects and can be used in the development of flexible state policy in financing national projects, taking into account the level of the target indicators achieved.