This paper examines empirically if the increase of funding uncertainty in government supported R&D institutes(GSRIs) in Korean cause managers to use more effective management control practices. Recently government introduced a new government R&D budget management system, based on competition, named PBS(Project Base System). Government requires GSRIs to be self-supporting and compete for funding from government. The introduction of new budget management system named PBS, has resulted in the increase of funding uncertainty in GSRIs. According to institutional theory, government organizations gain legitimacy by conforming to external expectations regarding management control practices, In contrast, contingency theory proposes that management control practices are driven by the fit between the technical features of the environment and the management control practices. The contingency literature provides that one external factor expected to motivate government managers to use more efficient control practices is the presence of competition and funding uncertainty. This paper use both theoretical perspective to develop hypotheses and examine the influence of funding environment on management control practices. Results show that the more institutionalized environment, the more managers in GSRIs rely on bureaucratic mode of control for conforming to external requirements, and the greater the funding uncertainty, the more managers use results and personal modes of control to improve research team performance.