Governance can be defined as a concept that encompasses a series of processes including partner selection as well as control and coordination of collaboration to achieve common goals. The study examined efforts to mitigate the risks of opportunistic behaviors into partner selection, partner relationship, control mechanism, and conflict management. For cases that have achieved commercialization outputs with the participation of SMEs, data was collected and analyzed such as interviews with project managers and case records for seven months from October 2016. According to the analysis result, as the complexity increases, such as multilateral cooperation for the development of finished products, cooperation with a trusted partner rather than a partner who can perform a task well was preferred, and the process control was put ahead of the output control. Regarding the partner relationship, the relationship between the owner and the agent differed according to the point of view, and there was a lack of clear allocation of authority and responsibility as well as a reward for the result. In terms of the conflict management, most emphasis was on resolving conflicts or difficulties, and no attempt was made to utilize the positive aspects of the conflict. The structure of most industry-university-institute cooperation organizations is simply composed of the host and participating organizations, and the management regulations should be amended for companies, that put actual funds and use the outputs, to have the authority and responsibility as the owners, and be allowed to use the governance elements appropriately to take the lead as consumers.