Some areas in Chongqing were hit by more than 260 millimeters of rainfall, said the headquarters.
The heavy rain sent the water level on the Yangtze River's small branches near the Three Gorges above the warning line. Meanwhile, Fangcheng River in Guangxi also reached a dangerous level.
The Donghe thermal spring hydrometeorological station reported a water level of 197 meters during the flood peak at 5 a.m. on Monday, 15 centimeters above the warning line.
The provinces and region mentioned above and the Inner Mongolia Autonomous Region, Shanxi, Henan, Guizhou, Hunan, Jiangxi and Yunnan provinces will likely see moderate heavy rain up to Tuesday noon, according to weather forecasts. Some areas will be hit by rainstorms, thunderstorms, strong winds or hail.
Meteorologists have warned people living in these areas to watch out for possible natural disasters such as flash floods, land slides and lightning strikes.