After the transition to program-targeted management methods in the Russian Federation, government programs have been actively developed at the federal and regional levels since 2013. Currently, it is of scientific interest what is the current state of these programs and how objectively they are evaluated using existing methods. Each region independently develops both government programs and methods of their evaluation. In this paper, using the example of the methodology for evaluating the effectiveness of the government program on Development of the Economy and External Relations in the Kursk region, the weights of the indicators of the government program in the final evaluation of the effectiveness of the program are calculated. For comparison, the results of calculations of the weights of the indicators of the government program for the Republic of Buryatia on Economic Development and Innovative Economy are given. The results obtained can be used in the development of methods for evaluating government programs at the federal and regional levels. The paper also shows the problems of creating government programs at the level of the subjects of the Russian Federation, such as a weak connection with the strategic goals of the socio-economic development in regions, an excessively large number of target indicators and their insufficient validity, high and insufficient validity of the weight indicators of individual subprograms and activities, and insufficient funding of programs in comparison with the stated goals. To improve the effectiveness of government programs, it is necessary to develop standards for such programs, as well as information disclosure standards, which would allow an independent assessment of their effectiveness.