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The governance of the higher education system is executed on three levels: federal, regional and municipal.

The Parliament (the Federal Assembly) of the RF is in charge of adopting federal legislation in the field of higher education and amendments thereof; setting levels of higher and post-graduate professional education; conclusion and ratification of international agreements regulating higher and post-graduate professional education; participation in the development and implementation of the state policy in the above areas; approval of the procedures for adopting federal/state higher education standards, of the procedures of employer participation in the development and implementation of the state policy in the field of professional education, etc.

The Ministry of Education and Science - the key federal authority - is responsible for  setting  education standards and  for policy making, including the financial policy and the legal regulation of the system of higher professional and vocational education. The Ministry has the right to submit to the RF Government legislative initiatives and draft laws. It also supervises the implementation of higher education legislation; in addition, it is in charge of the licensing and accreditation of the higher education institutions and their branches. The Ministry controls almost the entire budget (on average, every state higher education institution gets up to 70-80% of its funding from the state budget).

The higher education policy is implemented by the regional education administrations and higher education institutions that have significant autonomy and can adopt their own regulations and regional parliaments can adopt regional education legislation.

Within the structure of the Ministry, the Federal Inspection/Supervision Service in the sphere of Education and Science and the Federal Service for Intellectual Property, Patents and Trade Marks have been established. The Federal Inspection controls the implementation of legislation in the sphere of education, performs  quality control in education as well as licensing and accreditation of the higher education establishments and research organizations. It is responsible for the recognition of the degrees and qualifications in higher education.

Public higher education institutions are affiliated to and fall under the jurisdiction of  24 federal ministries that are the founders of state higher education institutions. These are: the RF Ministry of Education and Science (337 HEI), the Ministry of Agriculture (58 HEI), the Ministry of Health (52), the Ministry of Culture (45).

On the institutional level, the head of a higher education institution is the rector who is elected for five years term and has a number of deputy/vice-rectors responsible for specific activities and operational issues. Issues related to the development of the higher education institution are executed by the Academic Council that is elected for five years. The Academic Council comprises the rector (as chairperson), vice-rectors and may also include deans, faculty and student representatives.

The structure of higher education institutions is made up of  faculties that comprise smaller academic units called institutes, departments or chairs/units.