The introduction of marine protected areas (MPAs) in Australia has resulted in an increase in the number and total area of 'no-take' zones. The resulting closures impact all forms of commercial and recreational fishing in and around them despite international recognition indicating that Australian fisheries were already well managed according to ecological sustainable development guidelines. Furthermore, it is recognised within Australia that most MPAs are not designed to provide protection from the full suite of known threats that can affect biodiversity and long-term ecosystem viability. By directing MPA management disproportionately towards comprehensive no-take zones that affect fishing practices that are already required by state and federal legislation to adhere to sustainability requirements, the suite of threats affecting both protected and unprotected areas can be left inadequately and/or inappropriately managed. It is shown in this paper that the modified definition of the Precautionary Principle, which was developed specifically for the MPA process in Australia, is not in keeping with accepted international definitions and guidelines for the use of precaution. It is argued that the development of a definition of precaution to justify a predetermined output (MPAs) devalues the sound use of scientific principles and diminishes the conservation outcome. Furthermore, by distracting efforts from determining and managing the full suite of recognised threats, the value of what protection is provided in Australia's marine protected areas is eroded further.