Background: In 2011 the Agency for Public Health Education Accreditation (APHEA) was initially launched focusing on Master level (second cycle) education. Methods: Between 2012 and 2013 the Association of Schools of Public Health in the European Region, APHEA and partner schools conducted a study on the compliance of Master level programmes of public health to the accreditation criteria. A web-based survey of second cycle programmes of public health across 29 countries was conducted using the APHEA criteria. The 29 countries were categorized into four regions: Northern, Southern, Central and Eastern and Western. We applied a Chi square test to identify regional differences with regard to the compliance of the programmes to the criteria. Results: Data from 51 out of 71 schools contacted were analyzed. The compliance to the two themes of student and faculty exchange and quality management were lowest for programmes of public health throughout the EHEA. There were significant differences in the compliance between the regions with higher compliance in the Northern European region. Conclusions: Student and faculty exchange and quality management are essential for schools and programmes of public health to improve the quality of their education through expanding international knowledge and the pertinence of skills taught within European and national contexts. The results show that there are intrinsic issues with exchange and quality management as well as the role of national accreditation agencies in defining public health education for the future workforce.