The purpose of the article is to reveal the essence of the processes associated with structural changes due to market transformations in the agricultural sector, giving proper role to research in the innovation system to ensure the construction of a competitive economy. Research methods. The research is based on the existing provisions for the development of science, education and the latest technologies, the theory of agricultural production management, its sustainable development in the context of reforming and economic management, effective use and management of the country's agricultural enterprises. In accordance with the changes in the conditions of the functioning and structure of the agricultural market, the creation of interregional research centers was determined as a priority task on the way to improve the development of the agricultural sector. Research results. The main current problems of development of the agricultural sector and rural areas, which are interconnected and form part of the whole chain, are highlighted. At the same time, the essence of expanding the powers of sectoral departments and creating real opportunities for their self-development is emphasized. It is proposed to solve this problem by developing mechanisms for involving domestic agricultural science and exchange of experience in the field of management of research institutions, provided by the Agreement on European Integration. Scientific novelty. The essence of creating a system of innovation and investment development of NAAS in solving socioeconomic problems of rural development, which means strengthening the necessary institutional, legal and investment prerequisites for the development of appropriate infrastructure. Practical significance. The results of the study to improve the reform of agricultural science - the creation of interregional research centers NAAS, which is an important stage and will serve to address issues of building an effective system of scientific and innovative development of the agricultural sector and rural areas. Figs.: 3. Refs.: 14