This paper analyzes the organizational risks associated with modern mechanisms of state management for implementing the Russia’s Arctic strategy. An overview of the state management decisions in 2009–2012 is given. It is shown that the low effectiveness of the subprogram “Development and Use of Resources in the Arctic” in the Federal Target Program “World Ocean” was defined by the instability of state priorities in funding its projects; program faced high coordination risks. The multistage structure of management does not provide system monitoring of goals and consolidation of state and private investments. The strengths and weaknesses of the following three alternative concepts of state management of the Russia’s Arctic strategy are discussed: 1. improving the modern state mechanisms and establishing the Ministry of Regional Development of the Russian Federation as a federal commissioner and coordinator; 2. creating a public-private corporation Arktics where the state owns a controlling stake and providing it with wide powers to attract private investments for science and innovation projects; 3. organizing the project management of the Arctic development program as a set of interregional and territorial mega projects and creating a state committee that coordinates the decisions of the strategy’s participants at the Prime Minister level.