Research and development (R&D) project management involves managing multiple stakeholders with conflicting stakes. This article proposes a systems approach to capture such conflicting stakes of multiple stakeholders in controversial R&D projects. The approach is illustrated using a New Zealand case study related to the use of 1080 chemical for pest management. Initially, the problem situation was structured systemically by analysing the behaviour of the main variables and by conducting a stakeholder analysis. Further, a participative systems model related to the problem situation was developed using a group model‐building process. The analysis of the model revealed a set of feedback loops operating in the system identified as constituting and responsible for the complexity of the problem situation relating to 1080 use. In conclusion, the paper highlights some strategies suggested by the stakeholders to manage conflict.