The article revels the management issues of the modern stage of the government programs implementation in Russia using the example of the Russian Federation Government Program “Development of Science and Technology” for the period of 2013-2020 and also suggests their solutions. Transition from the ROR method to the Results-based budgeting at the RF budgeting by accepting long-term government programs causes the necessity of improving the methods for estimating their implementation. The article also considers the methods for efficiency estimate of the government programs applied in the USA (PART system). These methods are tested at estimate of the regional target program in the Ulyanovsk Region with the purpose of comparative analysis of the obtained results. Having investigated the reasons of non-correspondence of the Russian specialists’ estimate and the results of the conducted calculation and detecting the disadvantages of the current Russian methods, the authors have developed a suggestion to integrate the main criteria of the PART system into the Russian practice. They also revealed that despite such a positive role of targeted programs in the life of a state, their implementation in the RF practice is far from ideal, because both the regulatory base and the practice of its implementation require significant corrections. Imperfection of the Russian practice of targeted program approach to the government regulation is manifested in numerous repetitions of the events and measures in terms of various programs (projects) of the executive authorities, chronic lack of financing, long-standing time lag of their implementation, inefficient system of control over the achievement of the goals and the estimate of the justification of the budget costs. It is defined that considering the issue of development, implementation and estimate of efficiency of the targeted programs through the example of our country and moreover comparing it with the other countries it is notable that Russia have been implementing state policy in the conditions of market relations for just 20 years (considering the nonmarketable practice of state programming this period is certainly longer). The ways of the situation improvement are revealed and the planning trend lines on general increase in the government control efficiency are built up.

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