The advisory bodies of CEITEC BUT are:
- Scientific Council- approves degree programs, assesses and discusses the long-term educational, scientific, and research activities of the institute, the scope and the level of publishing activities, the level of cooperation of the institute with the faculties and other work from outside BUT. The council also monitors the institute's activities in line with the needs of state bodies, the cooperation of the institute with scientific, expert and professional associations.
- The Coordinating Council- discusses strategic issues related to the main activities of the institute, especially those that are related to joint activities and shared human resources with the Faculty of mechanical engineering, the Faculty of chemical and electrical engineering and the Faculty of ICT
- Laboratory Council - discusses matters relating to one of the major segments of the Institute's activities. construction, operation and development of laboratories
- The Study Programme Council
