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The outbreak of Covid-19 holds important lessons for general understandings of specialised agencies and their interactions with the political executive in a context of high political salience and uncertainty of the knowledge upon which agencies can base its professional decisions and pursue its policy preferences vis-à-vis the political principal. This case study analyses the behaviour of the Danish Health Authority (DHA) during two critical series of events in 2020 and 2021. Based on unique document access and interviews with key actors, the article makes a triple contribution to the literature on agencies by showing that: (1) interactions within the governmental hierarchy are transactional rather than rule-bound; (2) agency impact in interactions with the political executive depends on the agency head’s skill in forming a strategically neutral approach; (3) a strong agency reputation with key audiences is not sufficient for ensuring political influence or avoiding political interference. [ABSTRACT FROM AUTHOR]