This study analyzed the morbidity and mortality rates of the COVID-19 pandemic in different prefectures of Japan. Under the constraint that daily maximum confirmed deaths and daily maximum cases should exceed 4 and 10, respectively, 14 prefectures were included, and cofactors affecting the morbidity and mortality rates were evaluated. In particular, the number of confirmed deaths was assessed excluding the cases of nosocomial infections and nursing home patients. A mild correlation was observed between morbidity rate and population density (R2=0.394). In addition, the percentage of the elderly per population was also found to be non-negligible. Among weather parameters, the maximum temperature and absolute humidity averaged over the duration were found to be in modest correlation with the morbidity and mortality rates, excluding the cases of nosocomial infections. The lower morbidity and mortality are observed for higher temperature and absolute humidity. Multivariate analysis considering these factors showed that determination coefficients for the spread, decay, and combined stages were 0.708, 0.785, and 0.615, respectively. These findings could be useful for intervention planning during future pandemics, including a potential second COVID-19 outbreak.