Marked differences in COVID-19 mortalities have been observed among 47 prefectures in Japan. Here, we explored associations between COVID-19 mortalities and medical and public health capacities in individual prefectures. The following data by prefecture were abstracted from open resources provided by the Ministry of Health, Labour and Welfare in Japan as of May 24, 2020: total number of COVID-19 deaths; polymerase chain reaction (PCR)-positive ratio (i.e., number of patients with PCR-positive results/number of patients aiming diagnosis of COVID-19 or individuals in close contacted with COVID-19 patients); number of call centers, outpatient centers, and hospital beds specifically for patients diagnosed with COVID-19; and others. The primary outcome was COVID-19 mortality per million population. Multiple and simple linear regression models were applied. Two variables were significantly associated with COVID-19 mortality: PCR-positive ratio (P < 0.001) and number of critical care medical centers per million population (P = 0.001). PCR-positive ratio was positively associated with COVID-19 mortality (aR-sqr = 0.522). Low PCR-positive ratio, especially </= 4%, was associated with low COVID-19 mortality. Critical care medical centers may also play an important role in reducing the risk of COVID-19 death.