Background: COVID-19 has worse mortality than influenza in American and European studies, but evidence from the Western Pacific region is scarce. Methods: Using a large-scale multicenter inpatient claims data in Japan, we identified individuals hospitalised with COVID-19 in 2020 or influenza in 2017-2020. We compared patient characteristics, supportive care, and in-hospital mortality, with multivariable logistic regression analyses for in-hospital mortality overall, by age group, and among patients with mechanical ventilation. Findings: We identified 16,790 COVID-19 patients and 27,870 influenza patients, with the different age distribution (peak at 70-89 years in COVID-19 vs. bimodal peaks at 0-9 and 80-89 years in influenza). On admission, the use of mechanical ventilation was similar in both groups (1·4% vs. 1·4%) but higher in the COVID-19 group (3·3% vs. 2·5%; p<0·0001) during the entire hospitalisation. The crude in-hospital mortality was 5·1% (856/16,790) for COVID-19 and 2·8% (791/27,870) for influenza. Adjusted for potential confounders, the in-hospital mortality was higher for COVID-19 than for influenza (adjusted odds ratio [aOR] 1·83, 95% confidence interval [CI] 1·64-2·04). In age-stratified analyses, the aOR (95%CI) were 0·78 (0·56-1·08) and 2·05 (1·83-2·30) in patients aged 20-69 years and ≥70 years, respectively (p-for-interaction<0·0001). Among patients with mechanical ventilation, the aOR was 0·79 (0·59-1·05). Interpretation: Patients hospitalised with COVID-19 in Japan were more likely to die than those with influenza. However, this was mainly driven by findings in older people, and there was no difference once mechanical ventilation was started. Funding: Ministry of Health, Labour and Welfare of Japan (21AA2007).