Introduction: A compulsory research component is becoming increasingly common for clinical residents. However, integrating research into a busy clinical training schedule can be challenging. This study aimed to explore barriers to research supervision in specialist training programmes from the perspectives of clinical supervisors and trainees at a Malaysian university hospital. Methods: Qualitative interviews and focus group discussions were conducted (December 2016 to July 2017) with clinical supervisors (n=11) and clinical trainees (n=26) utilising a topic guide exploring institutional guidelines, research culture and supervisor-student roles. Interviews were transcribed verbatim and analysed thematically to identify barriers to research supervision. Results: Supervisors and trainees from 11 out of 18 departments participated. Both clinical supervisors and trainees struggled to successfully integrate a compulsory research component into residency training. Among the reasons identified included a lack of supervisory access due to the nature of clinical rotations and placements, clashing training priorities (clinical vs research) that discouraged trainees and supervisors from engaging in research, poor research expertise and experience among clinical supervisors hampering high-quality supervision, and a frustrating lack of clear standards between the various parties involved in research guidance and examination. Conclusion: Both clinical supervisors and trainees struggled to successfully integrate a compulsory research component into residency training. This was not only an issue of resource limitation since questions regarding clinical priorities and unclear research standards emerged. Thus, institutional coordinators need to set clear standards and provide adequate training to make research meaningful and achievable for busy clinical supervisors and trainees.