This paper analyses the system of national higher education public administration programs in the Czech Republic and Slovakia. It argues that current accreditation processes in these two new Central European EU member states are unlikely to help raise the quality of university public administration programs and their disadvantages may outweigh their advantages. Current accreditation is an ineffective and insufficiently transparent regulatory tool to decide fairly which institutions should and which should not have the right to deliver academic education. We suggest that a more goal-oriented, internationalized and quality based system should be developed.