Provision of independent scientific advice is central to the operation of regional fisheries management organizations (RFMOs) even though RFMOs are largely policy (and political) instruments. Political pressures and intervention in science and crossing of the boundaries between scientific and political processes, however, appear to be relatively common. A case study is presented to illustrate some ways in which this occurs. It involves a paper that was withdrawn from scientific meetings of two RFMOs as a result of largely political (rather than scientific) concerns. The details involved in this incident are important for understanding the ways in which political intervention in independent scientific process can and does occur. Moreover, unless one is directly involved in actions of this kind, it is impossible from the reports of RFMOs' scientific bodies to assess whether, and the extent to which, there has been political intervention in the scientific process. It is argued that the nature of the working arrangements in these scientific committees can engender deliberate or inadvertent crossing of the boundaries between scientific independence and the political processes of RFMOs, both of which are important components of RFMO operation. Further, there is very little documentation or assessment of the generic extent of such problems. No simple solutions or reforms exist for isolating scientific advice from political agenda in the processes of RFMOs but it is suggested that increased discussion of the problem along with better understanding and clarity of the role of science in the management process may lead to improved recognition of the importance of independent scientific analyses and advice.