A National Disaster Management and Mitigation Agency spokesman said, consecutive days of heavy downpour have bloated four rivers and destroyed their banks in Manado city, the capital of North Sulawesi province, since Wednesday and submerged the city, reported Xinhua.
The rain has also caused landslides in the Sangihe island of the province and buried several houses, said the spokesman.
"Temporary data shows 13 dead, two missing and 40,000 others taking shelters on safe grounds," Sutopo added.
He said besides Manado city, five other districts or cities in the province have been flooded, including Minahasa Utara, Tomohon, Minahasa, Minahasa Selatan, and Sangihe island, since Wednesday.
"Up to now (Thursday), there are no signs that the floods would recede significantly," an agency official said.
Emergency relief aids, including food packets, medicines, blankets, tents, rubber-boats and other equipment, have been sent to the affected areas, said the official.
Seasonal downpours have often caused floods in Indonesia, a chain of 17,500 islands, where over millions of people live in vulnerable flood plains, near rivers.