Modernization and technological development of economy of region, its passingto the innovative way of development requires not only the increase ofeffi ciency to use of accessible resources, creation of potential for innovative developmentbut also supposes serious organizational and structural changes in activity ofregional public authorities, responsible for realization of regional economic policy.Th e structure of the regional economic department in these terms must bebuilt not in accordance with the economic structure of the economy of the region(of a particular branch approach), but in accordance with the structure of the generatedincomes (project approach). The article considers some trends of perfection of the structure of regionaleconomic policy in new terms, transformation of its aims, tasks and functions,entailing change of approaches, methods of work and structural organization ofthe regional economic department, responsible for a success of its realization (anexample of the Karelia Republic).