This study investigated scientific research collaborations among universities in Northeast Asia and sought to conceptualize how they might influence, and be influenced by, broader processes of regional integration in economic, political, and societal arenas. To investigate these dynamics, a program for regional collaboration initiated jointly by the governments of China, Japan, and South Korea was taken as a case study. Co-authored publication outputs, annual project reports, and interviews with program participants at Japanese universities were analyzed using selected theories from the field of International Relations. The interviews explored the ideas researchers had about the potential for the indirect effects of collaborations to spill over into other arenas, and the barriers faced which impeded regional cooperation. The findings suggest that while a number of barriers exist, the program has contributed to ongoing knowledge production and regional collaboration, societal integration, and the cultivation of a generation of regionally-networked young researchers.