This study aimed to determine how behavioural restrictions due to the emergency declaration following the coronavirus disease 2019 (COVID-19) pandemic affect exercise tolerance and its outcomes in patients in Phase III cardiac rehabilitation programme. This is a multicenter retrospective cohort study. Participants in outpatient cardiac rehabilitation programmes and cardiopulmonary exercise testing before and after the emergency declarations were included. A total of 90 participants were included (median age 75.0 years, 69% male), and the changes in physical function and exercise tolerance were compared before and after the emergency declaration. Patients were divided into a decline-in-peak oxygen uptake (VO2) group and a nondecline-in-peak VO2 group. Comparison before and after the emergency declaration showed that the anaerobic threshold declined significantly and peak VO2 exhibited a downward trend. The decline-in-peak VO2 group consisted of 16 patients (17%) with better exercise tolerance, multiple comorbidities, and declined lower extremity muscle strength. These patients also had a higher rate of subsequent composite events (hazard ratio, 5.2; 95% confidence interval, 1.4–18.8, p = 0.01). Before and after the emergency declaration, the patient's exercise tolerance may decline, leading to a poor prognosis. This study suggests the importance of maintaining exercise tolerance during the COVID-19 pandemic.