The article defines the improvement of main directions of state regulation of port dues system operating in the Russian Federation seaports, in order to ensure economic feasibility, openness and transparency in establishing rates of port dues in accordance with the Russian Federation legislation. Following the results of world and Russian practice analysis of establishment and levy of port dues in seaports the authors propose their division into two groups: dues of public legal nature and payment for services of civil nature, rendering in the port. Instead of eight types of dues, which are currently established in the Russian Federation seaports, it is proposed to establish two port dues: tonnage and infrastructure, in order to facilitate the administration of payments between payers and payees of port dues. The tonnage due will be a source of monetary funds for financing costs for maintenance and operation of the seaports infrastructure facilities, and infrastructure dues will be an extra-budgetary source of monetary funds allocated for modernization and development of port infrastructure owned by the Russian Federation, and transferred to state unitary enterprises in economic management. There have been developed the algorithm and the method of calculating tonnage dues and infrastructure dues. The proposed algorithm for establishing dues of tonnage and infrastructure dues is based on the conceptual approach, which determines, that a key criterion for assessing the adequacy of levied amounts of port dues is the level of the seaport competitiveness. The use of this approach allows to optimally allocate the burden of the port dues payment in the Russian Federation seaports, in order to ensure financing costs on the maintenance and operation of port infrastructure, as well as its development and modernization.