This article is framed by the 900‐plus year old debate on the importance of academic freedom for democracy and human progress outlined by Karran. In particular, it discusses some contemporary threats to academic freedom in relation to the role of researchers and research institutes in the public policy process. Using a series of recent case studies of attempts to interfere with the publication of research findings in key sensitive policy areas of genetically modified foodstuffs, climate change, and agriculture, it is argued that while academic freedom plays a crucial role in relation to the development of public policies, it is currently under threat. This matter is discussed within a framework that allows the understanding of the relationship between researchers and the intervening State, the corporate and non‐government sectors with economic or social interests in any particular intervention, the media, and citizens. We apply the framework to recent cases in several controversial areas of policy that illustrate problems that have arisen. Moreover, we hypothesise that the problems have become more acute since the start of the era of privatisation and new public management with research agendas and targets often being increasingly set by policymakers. Finally, we draw some conclusions about the role of researchers and institutes in relation to agricultural and rural matters in modern democracies, arguing that freedom of speech and expression is an essential element in the policy role of researchers. At the root of this is the intensifying debate between representative and participatory democracy.