This article examines the experience connected with reforming the scientific and educational infrastructure of Kazakhstan from the standpoint of compliance with the principle of autonomy of academic science and teaching. First, the authors conduct a comparative analysis of international experience of integration of university education and research models and evaluate their applicability in Kazakhstan. Second, they discuss measures taken by the authorities, aimed at the creation of Kazakhstan’s shared scientific and educational space in terms of diversification of the higher education system. Third, they argue the need for strategic integration of the national education system with a network of institutions conducting basic and applied research. Finally, they suggest there is a need to combine the resources of individual research institutions and related institutions of higher education into a joint research and education center given maximum independence.