An important feature of innovation activity in Russia is the low level of inno-vative activity, despite the fact that one of the priorities of the economic develop-ment of our country defined the formation of favorable innovation climate and in-crease of innovation activity of the business. However, scientific-research and ex-perimental-design works require enormous costs and carry a high level of risk. As a result, despite the recognition of the inevitability of the innovation way of devel-opment in order to ensure economic stability in the conditions of financial instabil-ity, to innovate in Russia are sufficiently wary. The main reason for the current level of innovation activity of organizations is the lack of effective measures to en-courage innovation, and as a result, the lack of interest of private investors (includ-ing foreign) in investing in domestic innovation projects. For effective innovation requires appropriate his level of control aimed at ensuring the safety of investments and effective management. Accordingly, it was clarified the content of the infor-mation management innovation. Proposed allocation of separate cost accounting on innovation, oriented not only to provide information to external users (for external monitoring and analysis), but also internal (executives) for timely assessment of the efficiency of the innovation, internal controls and management decisions. Depending on the financial capacity of the economic entities defined forms of integration of organizational structures and allocated in accordance with the methods of accounting and innovation. Expedience of the use-case of managerial accounting system and the economic reporting.