摘要:A modified system of indicators for assessing the innovation activities effectiveness in the region based on data on patent and licensing activities in the framework of scientific and industrial cooperation is described. Also in the article we presented a general mechanism for innovation process effectiveness managing of such cooperative interaction. They are intended to be used as tools to support decision-making, allowing one to coordinate the cooperative indicators management. The proposed system of indicators provides transfer and decomposition of goals for planning operational activities by levels and actors of the innovation process in the cooperative formation, as well as monitoring their achievement. Taking into account the peculiarities of the innovation environment, the proposed balanced indicators system (hereinafter referred to as the BSC) focuses on non-financial logistics performance indicators and patent’s information. The structure of the BSC assumes a pyramid-layer structure, the number of elements of each layer is determined by the structural decomposition of the cooperative interaction corresponding level. The article describes stages of forming such BSC-maps process. As a tool for improving the balance of strategic maps for generating management decisions, a transition to “horizontal dynamics” is proposed, according to which at each level of logistics management, among all goals there is the greatest deviation from the target values, i.e., from the target values achieved to the least extent. These goals are the “target limitations” of the enterprise effective operation and they take greatest importance for further analysis of critical situations. For this purpose, a procedure for managing innovation environment by deviations is proposed.