Over the past several years, it has been pointed out that public research institutes are less productive than private ones; moreover, they need to clarify their roles in the development of Korea's national system of innovation. With a view to identifying the causes of problems in public R&D activities, this study examines three pairs of government-sponsored research institutes (GSRIs) and private R&D organizations in Korea; it compares their strategic goals, the roles of their top managers, their organizational characteristics, and the attitudes of individual researchers. The results, based on responses from 570 R&D managers and professionals in both sectors, reveal the following: compared with private R&D organizations, GSRIs 1) have relatively less dear strategic goals and R&D objectives; 2) their R&D activities are very broad and not well focused; 3) their top management plays a biased external role in order to gain institutional legitimacy; 4) their organizational structure tends to be more decentralized but less flexible; 5) their R&D work climates exhibit higher autonomy, cohesiveness, work-pressure, and risk-taking propensity, but display lower customer-orientation and less fairness in a reward system; and 6) the researchers are dissatisfied with their jobs and organizational incentive systems, and also less committed to the organization. As an attempt to understand the root causes of the salient features of GSRIs, this study further explores the impacts of external environments over the period of their development, including the government Science and Technology policy, the national project funding and accounting systems, and institutional regulations, on their internal management systems. Findings of distinctive managerial features of GSRIs and their relationships with external environments suggest several managerial and policy implications for designing more effective R&D management systems of GSRIs in Korea.