Analyses of pandemic preparedness policies revealed weaknesses in control systems of European nations. This reinforces the need to support countries in their endeavours to prevent and contain pandemics. A Hazard Analysis and Critical Control Points (HACCP) was applied to a generic plan to identify weaknesses in pandemic management policies, in order to develop recommendations for improving national pandemic management systems. Policy components considered in our analysis are command and control, early case detection and disease surveillance, and community containment management. The main critical areas identified in national pandemic control were: communication systems among all institutions and levels involved in pandemic management, guidelines and regulations describing how key personal and institutions should operate during a pandemic, training and dissemination of information to health care personnel involved in outbreak management. The HACCP analysis highlighted the need for agreed communication structures, clear division of responsibilities and harmonised policy guidelines at all levels of pandemic management. Being prepared is the key to successfully coordinate and implement response measures when a pandemic emerges.