Models on innovation, for the most part, do not include a comprehensive and end-to-end view. Most innovation policy attention seems to be focused on the capacity to innovate and on input factors such as R&D investment, scientific institutions, human resources and capital. Such inputs frequently serve as proxies for innovativeness and are correlated with intermediate outputs such as patent counts and outcomes such as GDP per capita. While this kind of analysis is generally indicative of innovative behaviour, it is less useful in terms of discriminating causality and what drives successful strategy or public policy interventions. This situation has led to the developing of new frameworks for the innovation system led by National Science and Technology Policy Centres across the globe. These new models of innovation are variously referred to as the National Innovation Ecosystem. There is, however, a fundamental question that needs to be answered: what elements should an innovation policy include, and how should such policies be implemented? This paper attempts to answer this question. Summary It is of no doubt that emerging techniques in the evaluation of R&D and measurement of innovation are finding a broad agreement across nations and regional groupings. However, it is very important for the science policy community across nations to be consistent with the taxonomy used. This paper focuses on the prospective tools, models and data used in this measurement and their importance to the development of a functional evidence-based platform for science and innovation policy. The various models of the National Innovation Ecosystem developed are reviewed and the gaps within these models are identified. The paper then defines a new architectural framework for a National Innovation Policy: The Ecological System of Innovation. In developing this framework the paper uses a hybrid of models, methodologies and concepts including, the Delphi Method, Balanced Scorecard, the Quadruple Helix Theory, and the Analytic Hierarchy Process. The Ecological System of Innovation framework is then used to address the fundamental challenges to the development of a functional evidence-based platform for science and innovation policy. Introduction Researchers have successfully explored the definitions of innovation, innovation theories, the rationale of government interventions on innovation, innovation policy instruments, and the relationships between new technologies, emerging markets, innovative services, and economic growth. However, there are different conceptions regarding what constitutes the core elements of a national innovation system and different scholars draw the borderlines of the system differently.