We evaluated the impact of the new coronavirus disease (COVID-19) on healthcare access in Japan in terms of the number of outpatients and hospitalized patients as well as the length of hospital stays, during the first wave of the pandemic, up to June 2020. This observational study evaluated the monthly average number of outpatients per day at hospitals, the average number of hospitalized patients per day, and the average length of hospital stays per patient, from December 2010 to June 2020, using the hospital reports data, which are open aggregated data on the utilization of hospitals from the Ministry of Health, Labour and Welfare. These numbers were compared with those from the same period of previous years, using a quasi-Poisson regression model. We found a nationwide decrease in the number of outpatients in general hospitals and hospitalized patients, particularly in long-term care beds in Japan, as well as the excess length of hospital stays among psychiatric care patients during the first wave of the COVID-19. This limited access to healthcare demonstrated the importance of the long-term health monitoring of vulnerable populations and the need for urgent management support to healthcare facilities in preparation for possible prolonged pandemics in the future.