Paper deals with the possibilities to improve productivity of domestic academic research through partnership cooperation between actors of innovations ecosystems at national and regional levels. Cooperation between academic research and business plays important role in this context. Main attention is paid to public sector of academic research; all problems are illustrated for the case of Novosibirsk oblast. The opinions of representatives of research institutes of Siberian Branch of Russian science Academy as well as of innovative companies’ leaders were analyzed and reviewed. Main barriers for partnership cooperation were presented basing on this review. It is pointed out that lack of confidence within cooperation between ecosystem actors and therefore limited positive experience of cooperation present significant problem. State support as well as direct financing and adequate institutional environment creation should be aimed to the elimination of these barriers.