Abstract: It is proved that one of the factors on increasing agro-industrial complex performance in the Far East of Russia is its functioning within the framework of innovation-oriented cluster systems. Cluster organization provides for the concentration and specialization of production with the formation in the closed cycles of production, storage, processing and sale of products based on the principles of integration using mechanisms of corporatization and cooperation to obtain competitive products from the cluster subjects and to improve profitability. The possibilities of adapting the world experience of cluster’s operation for the agro-industrial complex of the Far East of Russia are identified. The features of an agro-industrial regional cluster are specified. The innovative agro-industrial cluster model for the primorsky territory of the Far Eastern Federal District as a self-governing scientific and production association of manufacturers, enterprises engaged in receiving products and raw materials for storage and processing, manufacturers of technical facilities, equipment and other material and technological resources for production and processing of products as well as specialized research institutions that provide the transfer of innovation in production is elaborated. The defining vector of the innovation-oriented cluster system is to ensure the effective functioning and competitiveness of agro-industrial enterprises at three levels: micro, meso and macro. The indices of the cluster functioning efficiency estimation with taking account of the synergy effect are proposed. The advantages of clustering on the principles of public-private partnership for enterprises of primorsky territory are grounded.