Economics has looked at the decision process of politicians but the decision process of agency staff has primarily been the purview of sociologists. Agencies affect the final form of regulations, they may enforce or ignore regulations that exist, and they provide information to the political process. Policies recommended by economists for nonpoint source pollution control are seldom supported by government agencies. This study examined the relationship between preferences for a particular policy and perceptions of farmer cost, farmer resistance, efficacy in salinity reduction, fairness, and administrative costs. The latter were included to find whether transaction costs of implementing policies affect preferences and whether this could help explain the existence of current policies. To test this hypothesis, a survey of people working on the salinity issue in Western Australia was conducted and structural equation modelling was used to examine the relationship between perceived policy attributes. As expected, fairness had a direct and significant effect on policy preference and also affected farmer resistance and administrative cost. Administrative cost was also positively affected by farmer cost and farmer resistance. Interestingly, other analyses showed there was no direct effect between farmer cost and policy preference or between effectiveness and farmer resistance.