There are 47 higher education institutions (HEIs) in Latvia (IZM data, 2018), but the number of students every year becomes smaller. That leads to a necessity for consolidation of HEIs and optimization of their administrative structures. At the same time, higher education (HE) normative regulations apply new tasks and responsibilities for HEIs (e.g., the development of internal quality management systems, strategy management,-etc.) which require new administrative functions, structures and additional resources. These controversial circumstances aren't supportive for HEIs' institutional management to develop processes in accordance with management by objectives (MBO) approach and to reach goals and objectives in HE studies and research. The aim of the paper is to research problems which interfere the development of organizational structures in accordance with the MBO approach in HEIs in Latvia. The authors have used the results from the HEIs' survey (DU, LLU, LU, LiepU, RSU, RTU) and interviews (ViA, VeA, JVLMA, BA, RPIVA (since 2017 consolidated with LU), LSPA) in Latvia. The paper is developed using research of the promotional thesis "Implementation of management by objectives approaches at higher education institutions in Latvia" (Stefenhagena, 2017). The research of the promotional thesis was carried out from 2010 to 2017. The conclusion of the paper is that HEIs' organizational structures are fragmented, and there is a tendency of duplicating administrative functions and duties. In order to apply MBO approach, a more sufficient analysis of administrative functions, processes, goals and objectives have to be carried out. Horizontal instead of vertical (hierarchic) cooperation among administrative units is encouraged.