In this paper, the contribution of empirical economic analysis to evidence based science, technology and innovation policy planning is discussed based on two case studies, (1) financial supports to firm's R&D by subsidies or tax measures and (2) innovation system reform policy such as university and industry collaboration promotion. It is important to make a good balance of "theoretical rigidness", "practicality by addressing important issues" and "quality of dataset". In addition, the results from empirical analysis should be interpreted with substantial reservations in terms of the limitations of economic theory and datasets.