Torrential rain triggered the flooding Sunday into Monday, and the waters began to recede Thursday, the National Disaster Mitigation Agency said.
The floods triggered landslides causing the displacement, the Jakarta Post reported. Evacuees were taken to mosques, hotels, churches and schools.
"At least 13 residents were reported dead and two missing, while another 40,000 have taken refuge," the agency's information center head Sutopo Purwo Nugroho said.
The flooding impacted North Sulawesi, North Minahasa, Tomohon, Minahasa, South Minahasa and Sangihe islands.