ObjectivesWhile many pilot projects have provided proof-of-concept information on CDSS efficacy, they encompass disparate systems unable to fully realise digital transformation. A lack of system-wide guidance on CDSS integration limits the efficacy of even technically well-positioned systems. The objective of this study was to identify challenges and opportunities relating to CDSS implementation in Australia. MethodsOpting for a qualitative approach, we purposefully sampled at national and state levels policymakers involved in CDSS implementation in Australia. We completed 11 semi-structured interviews from March to June 2020. The data were analysed using reflexive thematic analysis. ResultsThe Australian digital health landscape for CDSS implementation appears to be fragmented, characterised by a lack of integration between clinical and technological elements. This fragmentation is exacerbated by the lack of a shared understanding and collaboration between key stakeholders, increasing the risk of conflicting interests. CDSS are usually designed for a particular clinical workflow, and a lack of interoperability reduces the information flow between systems. Most efforts to achieve data standardisation are limited to organisational or state-level programs, thus increasing the risk of uncoordinated care across organisations. Considering different stakeholder perspectives on the value of CDSS could help to foster sustainable partnerships between governments, organisations, and consumers. ConclusionOur findings emphasise the importance of three things, each underpinned by stakeholder engagement: developing a clear and shared vision for innovation, building clinicians’ skills and organisational capacity for change, and establishing a national consensus on data standards for interoperable CDSS.