The Section of Higher Education, Science and Research (III) is responsible for the implementation of the state's science policy in the field of research, development and innovation within the scope set out in the Competence Act and the Act on Support for Research, Experimental Development and Innovation of Public Funds (Act No. 130/2002 Coll., on Support for Research, Experimental Development and Innovation of Public Funds and on Amendments to Certain Related Acts (Act on Support for Research, Experimental Development and Innovation), as amended).

It is responsible for the international cooperation of the Czech Republic in research and development, including negotiations with the bodies and institutions of the European Communities. It is responsible for bilateral and multilateral international cooperation of the Czech Republic in research and development and for European integration in this area, both for negotiating the relevant contractual documents and for announcing, contracting and implementing programmes to support their implementation. It is responsible for the concept of support for large-scale infrastructure for research and development. It carries out activities in connection with the preparation and implementation of R&D programmes, including the conduct of R&D tenders, the award of public contracts and the evaluation of project and programme results. It also carries out the tasks necessary to evaluate the results of research organisations with a view to providing institutional support for research and development. It proposes rules and ensures the provision of support for specific university research. It cooperates with the Council for Research, Development and Innovation in the preparation of the National Policy for Research, Development and Innovation, in the preparation of the draft State Budget expenditure on research and development and in the creation and maintenance of the Research, Development and Innovation Information System. It shall also maintain a list of research organisations approved for the recruitment of researchers from third countries.