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Innovative development of the national economy provides qualitative transformation of the refining sector. In order to promote the depth of oil refining and the relative increase the refining share in oil extraction the Government of Russian Federation has changed the mechanism for calculating export duty on crude oil, light and dark oil. This research work addresses the nature of financial implications for the budget system in connection with these changes. Different effects are observed for oil extractors and oil refiners. Conclusions are reasoned by calculations.