Storms also snarled transportation, delayed flights, blocked highways and caused power outages in parts of the country.
Flash floods and landslides caused by the heavy rains have caused casualties and economic losses in 74 county-level cities in six southern provincial-level regions, including Fujian, Guangdong, Hunan, Jiangxi, Guangxi and Sichuan, the ministry said in a notice on its website on Thursday.
More than 2.56 million people have been affected and about 238,000 have been evacuated from their homes, the notice said, adding that more than 33,000 homes had collapsed or suffered damages.
The rains and ensuing floods and landslides have caused direct economic losses of 2.72 billion yuan ($398 million) with about 126,700 hectares of crops affected, among which 14,500 hectares had been destroyed.
The ministry and the Chinese National Committee for Disaster Reduction on Tuesday initiated a level-IV emergency response plan, dispatching work teams to guide the relief work in the three worst-hit provinces - Fujian, Guangxi and Sichuan.
More storms are forecast in the coming week in most parts of China due to the movement of a cold air front, Lin Jian, chief weather forecaster with the National Meteorological Center told China Daily on Thursday.
Generally the flood season in China begins in June and ends in September, during which heavy rains are common.
Floods and landslides in Fujian halted trains traveling between Fuzhou and Changsha, the Changsha Evening News reported on Thursday.
The No 1681 train from Changsha to Fuzhou was canceled on Thursday, and the No 1682 from Fuzhou to Changsha was canceled for Thursday and Friday, local railways bureau officials said.
The heavy rains also caused havoc in parts of north China.
Due to torrential rains and strong thunderstorms on Wednesday night and Thursday morning, Beijing Capital International Airport cancelled 415 flights and delayed 583 flights until 11 am on Thursday, with thousands of passengers stranded in the airport.
"My flight from Shanghai to Beijing was delayed by nine hours last night because of the bad weather in the capital, and thus I missed my United Airlines flight this morning," said Jon Gordon, a law student from Georgia State University.
The capital airport replaced the advertising screens with a live broadcast of the World Cup 2010 South Africa in the hall to alleviate passengers' anxiety.
Li Jiabao and Xin Dingding
contributed to this story.
CHINA DAILY
(China Daily 06/18/2010 page4)