BackgroundIn the German rehabilitation system, primary care physicians (PCPs), occupational health physicians (OPs), and rehabilitation physicians (RPs) fulfill different distinct functions and roles. While effective cooperation can improve outcomes of rehabilitation, the cooperation between these groups of stakeholders has been criticized as lacking or insufficient. This article proposes an approach to understand the low levels of cooperation by examining the role of group perception and group identity in intra-professional cooperation as a barrier to cooperation between physicians in different roles. Group perception was evaluated in terms of (1) negative views about another group of medical specialists and (2) differences between the perception of members and non-members of a medical specialty group. To examine this issue, we focused on the role of OPs in the German rehabilitation process.MethodsWe implemented a qualitative study design with eight focus group discussions with PCPs, OPs, RPs, and patients (two focus group discussions per stakeholder group; 4–10 participants) and qualitative content analysis. We used the Social Identity Approach by Tajfel and Turner as a theoretical underpinning.ResultsWhile all protagonists reported a positive perception of their own professional group, we found numerous negative perceptions about other groups, especially regarding OPs. Negative perceptions of OPs included 1) apparent conflict of interest between employer and employee, 2) lack of commitment to patient outcomes, 3) lack of useful specialized knowledge which could have a bearing on rehabilitation outcomes, and 4) distrust on the part of their patients. We also found divergent perceptions regarding roles, responsibilities, and capabilities among the specialist groups. Both negative and conflicting perceptions about roles were characterized as barriers to cooperation by study participants.ConclusionThis example of cooperation between RPs, OPs, and PCPs suggests that negative and diverging perceptions about an out-group could create barriers in intra-professional and inter-disciplinary cooperation between physicians. These perspectives might also be useful in explaining problems at intersections between different specialties. We suggest examining the inter-group dimension of perception-based barriers to cooperation in future interventions to overcome problems caused by intra-professional and inter-disciplinary conflicts in addition to other barriers (i.e. organizational hurdles).Electronic supplementary materialThe online version of this article (10.1186/s12913-018-3564-1) contains supplementary material, which is available to authorized users.