The subject of study in the article is methods, models and mechanisms of management of scientific activity of higher education institutions. The purpose of the work is to develop a conceptual model for managing the academic activity of higher education institutions based on the concept of triple helix interaction, P2M standard and risk management methodology. The following tasks are solved in the article: analysis of the model of the triple helix interaction of higher education institutions, business structures and the state in the implementation of innovation activities, research of the feasibility of applying the P2M standard for the management of scientific activity of institutions of higher education, development of a conceptual model of management of scientific activity in institutions of higher education taking into account the risk management system. The following methods are used: project and program management methods, systems theory and systems analysis, risk management methods. The following results were obtained: a conceptual model of management of scientific activity of higher education institutions was developed, which allows, on the basis of risk-oriented methodology, to take into account the interests of all stakeholder groups of the University-State-Business (U -S -B) triple system. Conclusions: The use of the conceptual model of scientific management of higher education institutions will allow taking into account the interests of all stakeholder groups in accordance with the P2M standard by integrating various projects and processes of their activities into a common innovation program. International experience demonstrates the effectiveness of translating the results of higher education research projects into practice, with the combined efforts of universities, business entities and government institutions. The presented participants form the triple coil system "University-Business-State", which we will call the system "U -S -B". This system integrates the processes of scientific activity, production and various forms of state regulation that interact. The U -S -B model has obvious advantages -science senses production needs, the state takes incentive measures, business structures adapt to the needs of the population in new goods, services or technologies. This paradigm assumes that new knowledge and technologies resulting from the scientific activity of higher education institutions are channeled into the sphere of business and public institutions.