Fisheries management is increasingly involving a wide range of stakeholders in the decision making process. However, in most fisheries, the set of management objectives are poorly defined, and the implicit importance placed on these objectives may vary considerably both between and within different stakeholder groups. This may lead to conflicts within management advisory groups where members from different stakeholder groups view potential management outcomes substantially differently, and inconsistencies in decision making when changes in stakeholder representation take place. In this paper, the institutional structure of fisheries management in Australia and the roles the different organisations play in shaping fisheries management plans are detailed. An explicit hierarchy of management objectives is developed in collaboration with key managers and policy makers. A large survey of stakeholders involved in Australian Commonwealth fisheries management was undertaken to determine stakeholder preferences relating to these objectives. The results highlight the differences in perspectives regarding the relative importance of the multiple objectives of fisheries management. While on average stakeholder preferences generally correspond with their expected preference set, the results also indicate that there is generally low coherence within stakeholder groups.