The delegation of public tasks to semi-autonomous or independent agencies is a typical manifestation of depoliticisation. Much of the literature focuses on explaining why delegation occurs, whereas much less is known about the dynamics of the relationships between agencies, parent ministries, and other stakeholders as they unfold in practice. The paper sets out to analyze these dynamics through the analytical lens of depoliticization with a specific focus on research agencies in Germany. This special breed of agencies is characterized by usually highly complex tasks (e.g. risk assessment for food and consumer products) which require a substantial amount of specialist expertise. Many of these agencies have their own laboratories and conduct research projects, also in collaboration with universities. These agencies operate in a grey zone between politics, administration, and science. This recently provoked some controversial debates in the wake of an evaluation of these agencies by an important scientific advisory body which recommended delegating more autonomy to those agencies and hence putting them further away from politics. The federal government’s support to these proposals was rather lukewarm; claiming that after all each ministry needs to decide what kind of research is needed in its policy sector. In day-to-day decision-making, the dual position of research agencies allows both politicians and agencies to refer to different logics of decision-making, depending on what is seen as most appropriate in a given situation. Thus, the general theme of the paper is “scientization” as a specific dimension of depoliticization. In empirical terms, the paper mainly draws on a large number of expert interviews within several agencies and their parent ministries.