The floods have torn down 48,000 houses and damaged 94,000 houses in southern China, and forced about 591,000 people to evacuate from their homes, the official said.
From Wednesday to Saturday, continuous torrential rains, mudslides and floods hit Hunan, Guangdong, Guangxi, Guizhou, Jiangxi and Fujian, affecting more than 8.97 million people.
The disasters have caused an overall economic loss of more than 2.9 billion yuan (371 million U.S. dollars), according to the ministry.
In Guangdong, heavy rains have killed 18 people and left four missing by 3 p.m. on Sunday, according to local authorities.
A total of 1.72 million people were affected in the province, which has evacuated 72,400 people from their homes. Floods have damaged 49 roads in the seriously affected Meizhou City, of which 29 remained closed to traffic by 7 p.m.
The death toll in torrential floods in south China's Guangxi Zhuang Autonomous Region has reached 13 and one remained missing by Sunday, according to local civil affairs authority.
More than 1.97 million people have been affected after the floods triggered by continuous heavy rains hit some 40 counties since last Wednesday.
According to the local civil affairs bureau, 9,200 houses were knocked down and 75,181 hectares of crops were affected, incurring 529 million yuan (about 70 million dollars) in direct economic losses.