The paper provides the data and analysis on innovative activity in the Russian Federation in the context of import substitution. To solve the problem of the effective functioning of the innovation process state regulation system under the conditions of import restriction, it is proposed to introduce an independent assessment system of an innovation competitiveness for the purposes of applying these forms of stimulating factors influence, and the maximum speed of adoption and implementation of a decision on it. The formula proposed for evaluation the efficiency of an innovation with the usage of the import substitution coefficient will allow the public and municipal bodies both to carry out an express assessment of innovations consistently and to minimize risks in spending public money. In order to implement the express assessment system of innovative activity it is proposed that the public management bodies monitor the assessment system of the investment climate condition on a certain territory and the target usage of allocated money and granted incentives at all stages of the innovation process.