In the era of the knowledge-based economy, centers of scientific excellence play a crucial role as engines driving technological development and innovation. This study conducts a comparative analysis of such centers in Australia and New Zealand and extracts policy lessons relevant to the development of science and technology in Iran. The research examines the policy dimensions, governance structures, and operational processes of these centers using a combined theoretical framework that integrates the Triple Helix model (university–industry–government) and multi-level governance. Findings reveal that Australia, with a strong emphasis on innovation and global competitiveness, employs a multi-level funding model and engages extensively with industry. In contrast, New Zealand adopts a more centralized and targeted approach, focusing on strategic areas such as quantum technologies and indigenous research. Both countries benefit from transparent evaluation and monitoring mechanisms, a combination of public and private funding sources, and dynamic stakeholder engagement. Based on the results of this study, several policy recommendations are proposed for Iran: the formulation of a national roadmap prioritizing key fields such as nanotechnology and biotechnology; strengthening university–industry–government interactions; and designing diverse funding models. Furthermore, the establishment of supporting institutions similar to the Australian Research Council (ARC) and New Zealand’s Centres of Research Excellence (CoREs), the development of practical educational programs, and participation in international scientific networks are also recommended. The study underscores the importance of adapting global models to local contexts and national needs as a key success factor for centers of scientific excellence.