Muammer Guler, Istanbul's governor, said more than 20 people were also injured in floods on Wednesday, and added that heavy rains were expected to continue throughout the week.
Anita McNaught, Al Jazeera's correspondent in Istanbul, said the poorer members of the city's community were the most affected by the flooding.
"A lot of the damage to Istanbul is in areas of recent construction, areas of rapid industrialisation.
"The blaming has already started in the municipality, with one minister saying that people had built their homes before they could properly put the infrastructure in place - they're talking about decent drainage and storm water."
She said the areas hit were "vulnerable to these uncontrollable, unmanageable weather events".
Severe weather conditions have caused two streams to swell and overflow, inundating dozens of homes and workplaces.
Waters are reported to have risen by more than a metre in Istanbul's Ikitelli district, with motorists climbing on top of their vehicles while waiting to be rescued.
Hikmet Cakmak, Istanbul's deputy governor, described the scene at Ikitelli as a "disaster" and said four helicopters and eight boats had been sent to help the stranded motorists.
Tayyip Erdogan, Turkey's prime minister, is due to travel to Istanbul on Wednesday to see the damage.
The Istanbul mayor's office said in a statement on Wednesday that about 900
firefighters and rescuers were working in the flood area, backed up by 220 vehicles and 30 inflatable dinghies.
The statement added that more than 1,000 people had been rescued since Tuesday when the rains first battered the western outermost suburbs of Istanbul before moving over the city.
Istanbul is situated on the steep banks of the Bosphorus strait, one of the world's busiest waterways and a major conduit for cargo ships and oil tankers from the Black
Elsewhere in northwest Turkey, two bridges were demolished by floodwaters on the Bahcekoy-Saray highway.