The article deals with the problem of implementing the goals and objectives of the innovative development of the economy as a national priority, and analyzes the indicators of innovative activities of organizations and enterprises over the past 10 years. Particular attention is paid to the problem of qualification imbalance, which is a significant constraint on achieving the set goals in the short and long term. A comparative analysis of competency-based models of the innovation economy has been carried out, allowing to overcome the qualification imbalance, and contradictions have been identified that impede the formation of innovative competencies in the system of higher education as a component of the national innovation infrastructure..