Implementation of various evaluation activities has been accompanied by fostering public research and innovation. This paper aims at describing characteristics and addressing challenges of evaluation system for research and innovation conducted in the public sector and on the basis of public funds in Japan. It explains the current legal framework for the R & D and innovation evaluation system. It elucidates that the Japanese public R & D and innovation evaluation system, getting out of the introductory phase, is pluralistic and stratified. It also points out that the evaluations for improvement of the quality of R & D from a long-term perspective have not been developed yet while those based on legal obligations or related to the survival and continuation of public research institutions have been prioritized. It furthermore mentions that the revised general guidelines for national R & D evaluation have still several issues. Then, it introduces the recommendations submitted by a working group for reforming the evaluation system. Finally, it provides normative suggestions, including articulation of evaluation and clarification and rearrangement of purposes, layers and objectives of evaluations, for a prospective framework of the evaluation system.