Hospital inpatient and emergency care settings provide frequent opportunities for clinicians to screen and provide brief interventions to patients who engage in harmful use of alcohol. However, these services are not always provided, with several reasons given in different studies. We aimed to systematically review clinician-reported barriers in the provision of brief alcohol screening, brief advice and intervention specific to hospital inpatient and emergency department settings. A systematic literature review was conducted of Medline, PsycINFO and CINAHL to identify the barriers perceived by healthcare workers in the provision of alcohol screening and brief intervention. These barriers were then categorized according to the Capability, Opportunity and Motivation (COM-B) model of behaviour change theory. Twenty-five articles were included in this study, which involved questionnaires, surveys, interviews and conference call discussions. The most commonly cited barriers (i.e. greater than half of studies) were related to Capability (lack of knowledge cited in 60% of studies); Opportunity (lack of time and resources, 76% and 52% of studies, respectively); and Motivation (personal discomfort in 60% of studies). Twenty-two other barriers were reported but with lower frequency. Clinicians cite a multitude of factors that impede their delivery of alcohol screening and brief interventions in the hospital inpatient and emergency department settings. These barriers were explored further under the framework of the COM-B model, which allows for intervention design. As such, changes can be made at the policy, managerial and educational level to address these barriers and help improve the self-efficacy and knowledge of clinicians who counsel patients on alcohol use.