Al Jazeera's Harry Fawcett, reporting from southeastern Fujian province on Sunday, said it was the first red alert issued this year.
Among the measures authorities were taking was enforcing stricter policing of traffic to keep people out of areas deemed threatened by landslides, which was the chief concern at the moment, our correspondent said.
A massive rescue and relief mission was already under way. In Fujian, soldiers could be seen wading through raging brown water to rescue students from an elementary school in Nanping city.
The government has estimated damage caused so far to be around $1.5bn.
The storms have collapsed reservoirs, overflowed rivers, caused landslides and power outages, and damaged highways, the China's disaster relief agency said.
Nine local officials in the Guangxi Zhuang Autonomous Region have been punished for dereliction of duty in flood work, including a reservoir monitor caught playing poker, the state-run China Daily said.