An important component of northern research in Canada has been a strong emphasis on local participation. However, the policy and permit landscape for community participation therein is heterogeneous and presents specific challenges in promoting effective partnerships between researchers and local participants. We conducted a survey of northern research stakeholders across Canada in order better to understand the benefits and challenges associated with research partnerships with a view to informing northern research policy and practice. We found that local engagement at the proposal and research design phases, the hiring of community researchers and engagement of local persons at the results dissemination phase were important factors affecting success. Respondents also indicated a lack of social capital (trust and reciprocity) between researchers and communities as placing a negative impact on science partnerships. Overall, researchers were perceived to benefit more from research partnerships than their community counterparts. Partnerships in northern research will possibly require further decentralisation of power to achieve the policy objectives of local community participation. This could be achieved, in part, by allowing non-academic principal investigators to receive funding, or by involving communities in research priority-setting, proposal review and funding allocation processes.