Agricultural systems have entered a period of significant disruption due to impacts from change drivers, increasingly stringent environmental regulations and the need to reduce unwanted discharges, and emerging technologies and biotechnologies. Governments and industries are developing strategies to respond to the risks and opportunities associated with these disruptors. Modelling is a useful tool for system conceptualisation, understanding, and scenario testing. Today, New Zealand and other nations need integrated modelling tools at the national scale to help industries and stakeholders plan for future disruptive changes. In this paper, following a scoping review process, we analyse modelling approaches and available agricultural systems’ model examples per thematic applications at the regional to national scale to define the best options for the national policy development. Each modelling approach has specificities, such as stakeholder engagement capacity, complex systems reproduction, predictive or prospective scenario testing, and users should consider coupling approaches for greater added value. The efficiency of spatial decision support tools working with a system dynamics approach can help holistically in stakeholders’ participation and understanding, and for improving land planning and policy. This model combination appears to be the most appropriate for the New Zealand national context.