This study explores crucial issues arising from the increasing establishment of supranational risk-governance systems that pursue a compromise between the need for effective governance and the necessity to avoid obstacles regarding trade. In these contexts, national public administrations become a peripheral module in a multilevel system where they see their organization altered and the legitimacy of their actions questioned. The analysis uses as a paradigm the systems on food safety controls and rapid alert in the EU and tries to answer the following questions: How do we give public administrations an effective role in the global scene? Are national administrations destined to become mere executors of supranational-set rules? Outcomes show that legal systems whose multilevel integration reached a high level suggest positive implications deriving from a new model of global governance not involving a reduction in state sovereignty, but leading it to a new role, guaranteeing the accomplishment of supranational-set goals and safeguarding the autonomy of national public administrations. Points for practitioners Practitioners, especially those who hold managerial positions, may often find themselves disoriented when acting in a multilevel context because of the shrinking of their autonomy as well as their submission to external rules and controls. Starting from the analysis of the elected paradigm, practitioners could find that in a well-functioning multilevel regulatory system, national public administrations are able to use their remaining range of discretion, even if minimal, in order to realize innovative organizational models, through which they may avoid direct intervention from upper levels and propose themselves as a model to be borrowed and applied in the whole system.