The increasing importance of measures under the so called "second pillar" of the Common Agricultural Policy of the European Union raises new challenges to decision-makers. The definition and operationalisation of goals as well as the implementation of concrete measures is a complex task. Decisions have to be made on priorities for goals and measures and finally on the allocation of the budget. In this article we demonstrate how policy-making in complex systems can be supported by co-operation between scientists, policy-makers and administrators. Using a participatory computer-aided programming approach the case of improving the agri-environmental programme of Saxony-Anhalt is examined. Based on interactive simulations together with stakeholders and considering the several determinants (like the level of co-financing, budget volumes and other restrictions for priority setting) the approach can substantially contribute to political strategy development.