Heavy rains caused Kali Kedung river over flowed and submerged over 5,700 houses and forced hundreds of residence to take shelters, the spokesman of the agency Priyadi Kardono told Xinhua over phone.
He said that two of the victims were killed after they were swept away by waters and the others were killed in lightning strikes.
"Searches were under way for the missing person," said Kardono.
Indonesia has been frequently hit by floods and landslides during the wet season which take places from December to April.
Decreasing forest-covered areas have been blamed for the disaster.