The paper analyses determinants of efficiency of Russian universities. The analysis is based on the data from annual monitoring of performance of higher education institutions conducted by the Ministry of Education and Science. Special attention is paid to the factors that are associated with public policy in the sphere of higher education. In order to explain the variation of the efficiency scores we implement one of the most modern techniques for analysis of efficiency’ determinants – Two-Stage Semi-parametric DEA. The high level of heterogeneity in Russian higher education sector is controlled for by considering two different specifications of DEA model: with the focus on educational activity and with the focus on scientific activity. The results show that relatively less efficient universities are more likely to be affected by the conside­red efficiency’ determinants compared to efficient ones. Universities that are governed by the Ministry of Education and Science and by regional governments appeared to be relatively more efficient compared to the universities that are governed by another federal authorities except for the Ministry of Education and Science (Ministry of agriculture, Ministry of Healthcare, Ministry of Culture, Ministry of Sport and so on). Governance by the Ministry of Education and Science has the strongest effect on efficiency level among considered factors. Governance by regional authorities has the weakest effect. The total square of buildings available for the university appeared to be positively and statistically significantly related to efficiency level. While the autonomous status has no any effect.