Public discourses have influence on policymaking for emerging health issues. Media representations of unfolding events, scientific uncertainty, and real and perceived risks shape public acceptance of health policy and therefore policy outcomes. To characterize and track views in popular circulation on the causes, consequences and appropriate policy responses to the emergence of Hendra virus as a zoonotic risk, this study examines coverage of this issue in Australian mass media for the period 2007-2011. Results demonstrate the predominant explanation for the emergence of Hendra became the encroachment of flying fox populations on human settlement. Depictions of scientific uncertainty as to whom and what was at risk from Hendra virus promoted the view that flying foxes were a direct risk to human health. Descriptions of the best strategy to address Hendra have become polarized between recognized health authorities advocating individualized behaviour changes to limit risk exposure; versus populist calls for flying fox control and eradication. Less than a quarter of news reports describe the ecological determinants of emerging infectious disease or upstream policy solutions. Because flying foxes rather than horses were increasingly represented as the proximal source of human infection, existing policies of flying fox protection became equated with government inaction; the plight of those affected by flying foxes representative of a moral failure. These findings illustrate the potential for health communications for emerging infectious disease risks to become entangled in other political agendas, with implications for the public's likelihood of supporting public policy and risk management strategies that require behavioural change or seek to address the ecological drivers of incidence. © 2012 Elsevier Ltd.