Malaria remains one of the essential public health problems in Indonesia. The year 2015 was originally set as the elimination target in Java Island, but there are still several regencies on Java reporting malaria cases. Spatial technology helps determine local variations in malaria transmission, control risk areas and assess the outcome of interventions. Information on distribution patterns of malaria at the sub-district level, presented as spatial, temporal, and spatiotemporal data, is vital in planning control interventions. Information on malaria transmission at the sub-district level in three regencies in Java (Banyumas, Kebumen, and Purbalingga) was collected from the Agency for Regional Development (Bappeda), the Population and Civil Registration Agency (Disdukcapil) and Statistics Indonesia (BPS). Global spatial autocorrelation and space-time clustering was investigated together with purely spatial and purely temporal analyses using geographical information systems (GIS) by ArcGis 10.2 and SaTScan 8.0 to detect areas at high risk of malaria. Our results show that malaria was spatially clustered in the study area in central Java, in particular in the Banyumas and Purbalingga regencies. The temporal analysis revealed that malaria clusters predominantly appeared in the period January-April. The results of the spatiotemporal analysis showed that there was one most likely malaria cluster and three secondary clusters in southern central Java. The most likely cluster was located in Purbalingga Regency covering one sub-district and remaining from the beginning of 2016 to the end of 2018. The approach used can assist the setting of resource priorities to control and eliminate malaria.