At the level of legislative and administrative power, the Riigikogu (Parliament), the government of the Republic of Estonia and the Ministry of Education and Research administer education system. A county, a local government and educational institutions have their specific roles in administering education system. The Riigikogu has the exclusive authority to:

• determine the principles of the formation, functioning and development of the education system;
• establish tuition fees for public educational institutions and universities in public law;
• decide on the establishment, merger, division and termination of the activities of  universities in public law.

The Government of the Republic has the authority to:

• adopt national education development programmes and provide guarantees for their implementation;
• establish the procedure for the establishment and reorganisation of public educational institutions and for termination of their activities;
• establish the tuition fees and rates for public educational institutions and universities in public law, and the procedure for remuneration;
• establish the maximum rate for study loans secured by the state;
• establish state concessions and benefits, including credit concessions, for pupils, students and educators;
• establish the Standard of Higher Education;
• approve the framework requirements for teacher training;
• grant educational institutions the right for provision of instruction in higher education and for awarding the corresponding academic degrees and diplomas.

The main function of the Ministry of Education and Research  is to ensure targeted and effective development of education, research, youth and language policy, and a high level and competitiveness of research and development.

For the achievement of its objectives, the ministry shall:

• plan, organise and develop education, research, youth and language policy; 
• develop national development plans in the areas of education, research, youth and language policy and ensure the compliance thereof with national and sectoral development plans; organise funding and implementation of development plans, and assessing the outcomes thereof; 
• exercise state supervision over teaching and education in educational institutions and the performance of national curricula and other educational standards;
• plan, develop national curricula and other educational standards and organise development and accreditation thereof.  

The Ministry of Education and Research is managed by the Minister, the Secretary General, and four deputy secretary generals: Deputy Secretary General for Higher Education and Research Policy, Deputy Secretary General for Pre-School and Basic Education, Language and Youth Policy, Deputy Secretary for Upper Secondary and Adult Education, and Deputy Secretary for Planning and Administration. See the structure and departments below.

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The personnel of the Ministry also includes the Minister's advisers and advisers of the Ministry, who are subordinated to the Secretary General or the deputy secretary generals.

In the area of government of the Ministry of Education and Research there is the Language Inspectorate, the main task of which is exercising supervision over compliance with the Language Act and other legal acts regulating the use of language, and the National Archives of Estonia, the task of which is to guarantee conservation of documented heritage, and Education Authority, the implementing body of Estonian education and youth policy.