Head of the Manado Disaster Handling Board (BPB), Johny Karinda, identified the victim as 72-year-old Engelbert Kambey from Mahawu sub district.
Floodwater had reached 1.3 meters, inundating hundreds of houses and forcing residents to seek temporary shelters on higher grounds and in mosques.
The flood has led to a house and a school in Paal Dua sub district being buried, Antara news agency reported.
Johny said that his office had distributed emergency aid, such as food and tents, to victims.
"We are monitoring [water levels] and have asked people to stay alert and move themselves to safer places," Johny said. (ewd)