The European Union (EU) inherited ‘indirect administration’ from classical international organizations: policies adopted by the international organization are subsequently to be implemented nationally by member states themselves, and not by bodies owned by the international organization. This arrangement has often led to legislation being incorporated and applied rather differently across countries. In order to harmonize implementation practices within the EU, we have witnessed a development from ‘indirect administration’ to more ‘direct administration’ in the sense that national agencies work closely with the European Commission, EU agencies and sister agencies in other member states, partly bypassing national ministries. Thus, stronger coordination across levels may counteract strong coordination at the national level. This ‘coordination dilemma’ seems to have been largely ignored in the literatures on EU network governance and national ‘joined‐up government’, respectively. The ambition of this article is twofold: first, the coordination dilemma is theoretically and empirically illustrated by the seeming incompatibility between a more direct implementation structure in the multilevel EU administrative system and trends towards strengthening coordination and control within nation states. Second, the article discusses organizational arrangements that may enable systems to live with the coordination dilemma in practice.