Introduction: The COVID-19 pandemic precipitated substantial disruptions in healthcare utilization globally. In Japan, reduced healthcare utilization during the pandemic’s early phases had been documented previously. However, few studies have investigated the impact of the pandemic’s later stages (2022–2023) on healthcare utilization rates, particularly in the Japanese context. Methods: We employed a quasi-Poisson regression model, adapted from the FluMOMO framework, to analyze temporal trends in Japanese healthcare utilization throughout the pandemic until November 2023. We estimated inpatient and outpatient volumes and hospital length of stay by bed type (general and psychiatric). Results: In general hospital beds, inpatient volumes remained significantly below pre-pandemic levels for every month until November 2023, with a reduction of 7.8 percent in 2023 compared to pre-pandemic levels. Psychiatric inpatient volumes, which had been declining before the pandemic, continued this downward trend, with the average occupancy rate decreasing by approximately 5.3% to 81.3% in 2023 compared to pre-pandemic levels. Significantly reduced outpatient volumes for both general and psychiatric care, in addition to prolonged lengths of hospital stay for psychiatric beds, were observed sporadically for several months in 2022 and 2023, persisting beyond the cessation of state of emergency and quasi-state of emergency declarations. Conclusion: The COVID-19 pandemic fundamentally altered healthcare utilization patterns in Japan. We observed a sustained reduction in general and psychiatric inpatient volumes relative to pre-pandemic baselines nationwide. The prolonged impact on healthcare utilization patterns, persisting beyond emergency measures, warrants continued monitoring of service delivery.