EU law places a number of requirements on administrative authorities that puts them in potentially invidious positions; while EU law today does not require institutionally independent administrative authorities or provide protection for the independence of authorities beyond the field of data protection, it does require administrative authorities to act independently through the loyal and effective enforcement of EU law. This requirement of acting independently without institutional independence raises certain implications for the role of administrative authorities acting within the hierarchical administrative orders of Member States. Using the case of Sweden – a Member State where administrative authorities enjoy significant constitutionally protected independence in the application of law and decision of cases – this article argues that the effect of EU law obligations of effectiveness and loyalty is a weakening of the hierarchical influence of the government over its own authorities, with a resulting shift of influence towards the legal arena through the provision of politically expedient interpretations of EU law. The invidious position of administrative authorities within the scope of EU law is likely to make them vulnerable to such influence, which may ultimately interfere with the effective administration of EU law.