As much as 19 inches of rain has been dumped on several cities since Thursday, including the scenic resort city of Guilin in the Guangxi region, the ministry said.
More than 11 million people in 11 southern provinces were affected by floods, landslides and hailstorms, the ministry said. Rivers have broken their banks, inundating surrounding communities.
A man was rescued from the rushing water after crews lowered a fire extinguisher tied to a hose to help the man trapped in the flood. He was eventually pulled to safety.
The ministry said water levels in major rivers and lakes in the southern province of Hunan have surged to alarming levels, and that the collapse of levees forced large-scale evacuations.
Dozens of flights at several airports serving major cities in the region including Chengdu, Changsha, Guangzhou, and Shenzhen were canceled or delayed, stranding thousands of travelers. Chengdu's airport was shut down for more than an hour Monday because of rain, forcing 13 incoming flights to land elsewhere, according to state media reports.
Trains also were halted, and roads were cut off to many towns and villages in the region. Television footage showed major flooding in cities, where the lower floors of homes and shops have been submerged.
The national meteorological center forecast more rain to come this week in southern China.
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