A tropical depression has been dumping torrential rain in central and southern Taiwan since Thursday, with some districts receiving close to 1,000 millimetres (39 inches) of rainfall.
Six have died in the storm so far, according to government figures, including three who were killed by a falling scaffold in the southern city of Kaohsiung. Almost 100 more were injured.
More than 6,000 people were evacuated with more than 1,100 still in shelters on Saturday morning, officials said.
Images showed residents in Kaohsiung and nearby Tainan wading in knee-deep water, as well as soldiers in central Chiayi county carrying elderly residents and children from their flooded homes.
Television footage also showed scooters and cars half-submerged in water and roads blocked by landslides.
Although the depression has already moved northwest away from Taiwan, floods have yet to recede in many areas.
Taiwan's weather bureau said the severity of the downpour was "extremely rare".
The island is frequently hit by typhoons in the summer. Last year more than 100 people were injured when Typhoon Nesat battered the island, causing flooding and widespread power outages.