The aim of the article is to analyze the modern state of university management systems and possible scenarios of their transformation. Methodological framework of the analysis is based on G. Minzberg approach and his typology of management system structural configuration. Conducted in 2003-2005 and 2016 research in the area of organizational culture state and interviews with experts and lecturers on the topic of university management organization challenges in 2017 allowed for identifying the shifting of management systems transformation direction towards mechanical bureaucracy, which means that universities entered a degradation scenario of university management system change. Key signs of this scenario formation are: - strengthening of formalization in managerial relation at the university; - increase of social distance between university administrators and academic staff; - decrease of trust towards administration among lecturers and researchers; - decrease of organizational and structural diversity of academic environment, stronger unification of university organizational structures. The article looks into prerequisites and conditions for developing other scenarios of university management structure transformation, evaluates possible risks and opportunities. The article is of a problem type and is addressed to researchers and university executives.