Organization of efficient economic activity in the Arctic zone requires development of human potential, transport infrastructure, exploitation of natural resources under the conditions of greatest possible environmental safety. In order to choose preferable trends of economic development and to provide efficiency of operations in the Arctic zone it is crucial to perform research in the areas of industrial efficiency upgrading and rational use of fuel, energy, mineral, chemical and biological resources of the Ocean and littoral areas of Russian Arctic. The paper analyzes major trends in the research on increasing economic efficiency of operations aimed at territory development in the Arctic zone. The authors justify the need to examine economic problems of rational resource use in the Arctic zone of Russia based on the proposed system of resource-estimation indicators and their application in establishing a mechanism of rational resource use with a due regard to protection of the marine environment. The paper also focuses on methodological problems of the target programme approach to complex development of the Arctic zone, creation of target programmes, industrial development and rational use of natural resources. The authors give rationale for the key task in this area – development of methodological principles of forming federal and regional target programmes, aimed at exploration, exploitation and rational use of natural resources in the Arctic zone of Russian Federation. An analysis is provided that focuses on the problems of creating a scientifically justified hierarchical system of programmes and regional regulations, creation of a scientific information data bank and other methodological issues.