More than 1.27 million people have been evacuated in the hardest hit regions, with large swathes of farm land submerged.
Economic losses already amount to over 10 billion yuan ($1.45bn).
Over 17.8 million people had been affected by flooding brought on by the torrential rains, while over 141,000 homes had been wrecked or damaged, officials said.
The rains have washed out roads throughout the nine provinces, many of which have also been hit by landslides, the state run Xinhua news agency said.
Rising food prices
Guangdong province has been the worst affected with at least 28 people there dead or missing. Xinhua reported that flooding in the Pearl River delta has been the worst in decades.
The Guangdong government issued an emergency flood alert throughout the province as levels in tributaries to the Pearl river hit warning levels, the report said.
In parts of Guangdong, up to 415 millimetres (16.6 inches) of rain fell in a 24-hour period from Friday to Saturday.
Food prices, the main cause of inflation in China, are rising due to the floods.
Vegetable prices in some Guangdong cities have risen between 30 percent and 70 percent on Saturday alone, Xinhua said.