BackgroundThe coronavirus disease 2019 (COVID-19) pandemic has affected the treatment system of medical institutions across the world. Studies of the populations and patients have reported mental health problems caused by the pandemic. However, there are few large-scale studies that have examined the effects of the COVID-19 on diseases from the perspective of psychosomatic medicine. The purpose of this study was to examine changes made to the psychosomatic treatment system of Japan during the COVID-19 pandemic and the impact of the pandemic on patients with diseases treated in psychosomatic medicine.MethodsWe conducted a nationwide questionnaire survey of members of the Japanese Society of Psychosomatic Medicine and the Japanese Society of Psychosomatic Internal Medicine from December 24, 2021 to January 31, 2022.ResultsOf the 325 respondents, 23% reported restrictions in initial outpatient admissions, 66% implemented telemedicine, 46% reported a decrease in outpatient admissions, and 31% working in facilities with inpatient units reported decreased inpatient admissions. To reduce in-person visits, 56% of the respondents decreased the frequency of patient visits and 66% introduced telemedicine. Seventy-eight percent of the respondents reported that the COVID-19 pandemic affected the onset or exacerbation of diseases treated in psychosomatic medicine, including psychosomatic disorders, anxiety disorders, mood disorders, adjustment disorders, and eating disorders.ConclusionsThis study revealed that the COVID-19 pandemic might have affected the practice of psychosomatic treatment in Japan and that various alternative measures were taken to prevent infection. In addition, although the items in this study were not compared to pre-pandemic data, the COVID-19 pandemic, it could have significant psychosocial effects on Japanese patients requiring psychosomatic care. Furthermore, respondents believed that numerous psychosocial factors were behind the impact of the COVID-19 pandemic on patients with diseases treated in psychosomatic medicine.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13030-023-00279-0.