The dead included seven women who drowned in a minibus taking them to work on Wednesday, the Anatolian news agency said.
Mustafa Demir, Turkey's procurement minister, said on Wednesday: "We are saddened by the loss of lives. There are still some people missing and we are searching for them.
"There is huge damage to infrastructure."
Sources told Al Jazeera that 31 people had been killed in two days, including 21 in Istanbul and two in Tekirdag province on Wednesday.
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.
"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.
Source: Al Jazeera (English)