Most successful control or eradication programs have been implemented in uninhabited regions, where little or no consideration of socio-political factors has been required. A considerable challenge for invasion scientists and decision-makers lies in controlling and eradicating species from inhabited regions, where challenges related to community stakeholder perceptions of the need to act, animal rights and uncertainty surrounding the presence and abundance of invasive species can threaten program development and implementation. We interviewed senior policy advisors and scientists who developed and implemented European red fox eradication policies on the inhabited island state of Tasmania, Australia. Our aim was to understand how they perceived that scientific evidence and community stakeholders’ knowledge and preferences should be involved in developing and implementing policy for fox detection and eradication. Respondents perceived that scientific evidence was best used in determining the need to act, assessing risks, designing eradication operations and monitoring progress. Overall, they perceived that involving community stakeholders was important in creating socially acceptable eradication operations that enable access to private land to implement eradication options. Community stakeholders’ knowledge was perceived, largely by scientists, to be based on misinformation, misconceptions and mistrust in science and, therefore, of limited value in informing policy. Community stakeholders were therefore not viewed as equal partners in the policy-making process by scientists. Only those stakeholders who performed a clear function were considered valuable. We propose that increased likelihood of successful eradication of invasive species from inhabited areas can be achieved by using a functional approach to stakeholder inclusion, to prevent dissent and conflict by legitimizing varied knowledge and capacity, leading to co-production of knowledge within a co-management governance system.