In this article, we first present an inductive taxonomy of national R&D structures in terms of relative R&D flows among prime actors. The R&D structure of Korea, along with the Japanese one, turns out to be an ill-balanced one characterized by the dominant role of private sector, vis-a-vis the minimal share of public R&D. In nature, private R&D is sensitive to business cycle and the vulnerability of the Korean structure has been invisible under prosperity but now is disclosed under depression. This problem is nothing new and indeed has long been recognized by the Korean government but the prescription seemed almost impossible. Ironically, the current economic crisis of Korea renders an unexpected opportunity for structural reform. As private firms are cutting down R&D investment, the relative share of public sector becomes significant. A simulation predicts that balanced systems will be achieved in some years if public R&D budget is kept up. Although the contraction of private R&D is by no means desirable, it is the right time for the Korean government to expand public R&D. Public R&D should be considered not only a remedy for market-failure but also a shock-absorber against cyclic instability. This is why the balance between public R&D and private R&D is emphasized.