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The Covid-19 pandemic during its early phases posed significant psychological threats particularly for medical frontline personal. It is unclear whether the medical workforce with the passage of time has adapted to these threats or have generalized to wider medical settings. An online survey was conducted reaching 1476 physicians in Germany with valid data from 1327 participants. Depression and anxiety were screened with the PHQ-2 and the GAD-2. Among a subtotal of 1139 (86.6%) physicians reporting personal treatment experiences with Covid-19 patients, 553 (84.8%) worked in a private practice (PP) and 586 (88.3%) in a hospital (HP). Covid-19 provoked profound conflicts between professional and ethical values: more physicians in PPs than HPs reported external constraints on their medical care being in conflict with the code of medical ethics (39.1 vs. 34.4%, p < 0.002) and significantly more HPs failed to maintain the dignity of their patients during the pandemic (48 vs. 27%, p < 0.0001). Comparison with reference groups among physicians with comparable size and settings during the first wave of Covid-19 revealed a significant increase in the prevalence of depression (23.0%) and anxiety (24.16%). Feelings of helplessness (63.3% in HPs and 53.4% in PPs) were associated with female sex, minor years of medical experience, sleeping problems and being encountered to unsettling events. Exposure to unsettling events and helplessness was significantly mediated by sleep disturbances (ß = 0.29, SE = 0.03, p < 0.0001). Covid-19 induced stress job content issues have broadened to medical disciplines beyond frontline workers. Emotional perturbations among physicians have attained a critical magnitude.