This cross-sectional study aimed to clarify how cognitive biases and situational factors related to diagnostic errors among physicians. A self-reflection questionnaire survey on physicians’ most memorable diagnostic error cases was conducted at seven conferences: one each in Okayama, Hiroshima, Matsue, Izumo City, and Osaka, and two in Tokyo. Among the 147 recruited participants, 130 completed and returned the questionnaires. We recruited primary care physicians working in various specialty areas and settings (e.g., clinics and hospitals). Results indicated that the emergency department was the most common setting (47.7%), and the highest frequency of errors occurred during night-time work. An average of 3.08 cognitive biases was attributed to each error. The participants reported anchoring bias (60.0%), premature closure (58.5%), availability bias (46.2%), and hassle bias (33.1%), with the first three being most frequent. Further, multivariate logistic regression analysis for cognitive bias showed that emergency room care can easily induce cognitive bias (adjusted odds ratio 3.96, 95% CI 1.16−13.6, p-value = 0.028). Although limited to a certain extent by its sample collection, due to the sensitive nature of information regarding physicians’ diagnostic errors, this study nonetheless shows correlations with environmental factors (emergency room care situations) that induce cognitive biases which, in turn, cause diagnostic errors.