In a modern economy clusters are the most promising form of integrating all types of resources: intellectual, material, financial, which provides competitive advantages to all participants of a cluster who complemen each other by knowledge, skills, and professional competences. Clustering is one of the most important preconditions for innovative activity in a region, increasing its competitiveness. Flexible control and the presence of many indirect connections can significantly enhance the innovation processes in the region. Creating innovation clusters in Russia is not so fast as in the developed countries such as USA, Japan, or Sweden, Germany, Austria, France and other EU countries.. Therefore, many aspects of their formation in the Russian regions require generalizations, detailed analysis and identifying the issues that will enhance the effectiveness of innovation clusters. This article attempts to analyze the existing systems of managing innovative regional clusters. It was determined that there are two main types of management structures of innovation clusters in Russia. One of them is based on creating the Board of a cluster, the second on establishing a center of cluster development in the region. The strengths and weaknesses of these types of controls, as well as of the mixed types of governaningstructures were also revealed. All this has allowed to identify the problems associated with using various systems of management of innovative territorial clusters in Russia, solving which will improve the efficiency of these clusters and thus the competitiveness of the Russian regions.