Consecutive days of heavy rain was blamed for the natural disaster since Sunday, spokesman of the agency Priyadi Kardono said.
"The waters have submerged 5,563 houses and predicted more than 20,000 people have escaped the floods," he told Xinhua.
The waters had also submerged roads to airport, causing no flight since Monday morning, Kardono said. "The access to the airport has been inundated," he said.
Flood is common in Indonesia after a heavy rains due to lack of forest-covered areas caused by forest destruction.