Beside the standard grant research projects are the individual research groups of Institute of Physiology CAS involved in the solving the prestigious Centers of Excellence (GA ČR) and the Center of Competence (TA ČR). These projects represent a consortium of several teams focused on innovative research in the field.

Institute of Physiology CAS is currently coordinating two Centres of Excellence: "Project of excellence in the field of neuroscience" (2012-2018) and "Centre of mitochondrial biology and pathology - MITOCENTRE" (2014-2018). Institute of Physiology is also involved in other centers in the role of co-recipient: "Preparation, modification and characterization of materials by radiation" (2012-2018) and "Center for Development of Original Drugs" (2012-2019).

Institute of Physiology is the main coordinator of the programs "QUALITAS - Wellbeing in health and disease" and "Preclinical testing of potential pharmaceuticals" which are the part of the Strategy of Czech Academy of Sciences AV21: "Top research in the public interest".