At a time when standardisation is increasingly recognised as an important area of innovation policy, the emergence of cyber-physical ‘smart systems’ presents significant challenges. Such complex technological systems have unprecedented levels of complexity and interoperability requirements, and pervade many critical national infrastructures, so calling for active roles for government to support their effective standardisation. Existing literature, however, offer limited insights into where, why, and how policy intervention can address the evolving variety of innovation challenges associated with standardisation. This paper thus proposes a novel innovation systems-based framework, for structured analyses of complex dynamics between standard-related innovation problems, relevant roles of government, and appropriate policy instruments. The historical case study of photovoltaic technology (from its early R&D to integration into Smart Grid) illustrates the framework, and provides practical implications for policymakers, suggesting evolving roles of government in the transition to cyber-physical smart systems in response to growing risks of systemic problems.