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Abstract Background Harmful alcohol consumption in Germany is a serious public health problem: About 7.7 million adults in Germany can be classified as risky alcohol consumers, about 74,000 deaths per year are related to alcohol consumption, and about 1.8 million adults in Germany (18–64 years) are classified as alcohol dependent. A treatment rate of 9% of all alcohol dependent patients in Germany implies a lack of supply and misuse of medical care. The aim of the study was to examine whether family practitioners (FPs) and psychiatrists have sufficient skills to diagnose and treat patients with alcohol problems. Methods A total of 6324 FPs and psychiatrists in the states of Saxony and Rhineland-Palatinate in Germany were invited to participate in this survey. Nine hundred seventy-four participants (90.3%/FPs) could be included in the statistical analysis (response rate: 14.3%/FPs, 21.6%/psychiatrists). Data was analysed descriptively and logistical regressions were used to identify predictors for physicians’ ability to feel adequately trained to diagnose and treat patients with alcohol problems. Results In comparison to psychiatrists, less FPs reported feeling sufficiently trained to counsel patients with alcohol problems (81.5% vs. 44.8%). Regression analysis revealed that FPs who felt not adequately trained had less experience with patients with alcohol dependence (OR 7.4), had attended fewer hours on alcohol addiction in continuing medical education (OR 4.8), and were more likely to be female (OR 1.9). A minimum of 10 h of training was associated with improved self-assessed competence. Conclusion Harmful drinking is a serious public health problem, and patients with alcohol dependence represent a large and demanding patient group in primary health care setting. Our study shows that the lack of training is a severe barrier in the work with this patient group in the primary care setting.