AIM: To clarify the association of cluster number and size of coronavirus disease 2019 (COVID-19) in long-term care (LTC) hospitals/facilities, general medical/welfare facilities and non-medical/welfare facilities with morbidity and mortality in 47 prefectures during 16 January to 9 May 2020 in Japan. METHODS: Information on COVID-19 clusters (n >/=2), and morbidity and mortality of COVID-19 was collected. RESULTS: A total of 381 clusters with 3786 infected cases were collected, accounting for 23.9% of 15 852 cumulated cases on 9 May 2020. Although the cluster number (/10(7) subjects) in LTC hospitals/facilities was significantly smaller compared with those in the other two groups, the cluster size in LTC hospitals/facilities was significantly larger than that in non-medical/welfare facilities. Cluster numbers in general medical/welfare facilities and in non-medical/welfare facilities were significantly positively correlated with morbidity (/10(5) ), indicating relatively early identification of clusters in these facilities. Unlike in these facilities, cluster size in LTC hospitals/facilities was significantly positively correlated with morbidity, indicating that clusters in LTC hospitals/facilities were finally identified after already having grown to a large size in areas where infection was prevalent. Multivariate logistic regression analysis showed that both cluster number and cluster size only in LTC hospitals/facilities were independently associated with higher mortality (>/=median 0.64/10(5) subjects) after adjustment. CONCLUSIONS: Preventive efforts against COVID-19 outbreaks even at the early phase of the epidemic are critically important in LTC hospitals/facilities, as both the larger number and size of clusters only in LTC hospitals/facilities were independently linked to higher mortality in prefectures in Japan. Geriatr Gerontol Int 2020; 20: 715-719.