The behavior of academic researchers who engage in cooperation with industrial partners has already been the subject of considerable research. A lack of understanding exists regarding the motivations of scientific research groups to engage in cooperation with other types of external non-academic organizations and the perceived barriers that may inhibit this activity. In this paper we analyse the motivations and perceptions of risks that shape scientific research groups’ cooperation with industry and government partners. We find that motivations to cooperate are partly dependent on the type of partner organization involved, with advancing research goals mainly acting as an inducement to cooperate with government agencies, while searching for opportunities to apply knowledge motivates partnerships with firms. We also find that the majority of research groups cooperate with both firms and government, with their major motivation being to apply their knowledge. Among research groups that only cooperate with firms, interaction effects between motivations influence the likelihood of cooperation. Research groups do not consider risk to scientific autonomy a barrier to cooperating with firms, while risk to scientific credibility inhibits cooperation independently of the type of external partner. However, being motivated to advance research can reduce the effect of perceived barriers, independent of the type of partner organisation.