The organisational structure of universities follows particular models that distinguish them from other learning institutions. This research investigated the effect of the organisational structure on the management of universities in Uganda using a sample of 361, 44% of whom were members of academic staff, and the rest contained university top management officials, administrative and support staff of universities. The subjects were selected using stratified random sampling. Data were collected using a questionnaire as well as interview guide. Statistical data were analyzed by referential and descriptive statistical processes with SPSS software. The findings reveal that the organisational structure of universities significantly affects the management. While the staff in universities require a more flexible approach which enhances more creativity, innovations and autonomy, the present organisational structure of universities contains high levels of formalization characterised by rigidity and centralised decision making processes. The staff feel that universities can operate between the two theoretical polarities (bureaucratic and collegial) in order to remain competitive.