Incessant rainfall since June 30 has destroyed 22,000 houses and forced 726,000 people to relocate in many provinces including Jiangsu, Hubei, Henan and Sichuan, the Ministry said.
Floods have also damaged crops, roads, telecommunication and electricity facilities, stopping traffic and delaying trains in some regions, it said.
The rains have resulted in an estimated economic loss of USD 3 billion.
The seasonal rains, known as the "plum rains" or Meiyu-baiyu rains, cause heavy flooding in China every year, usually affecting the country for around two months beginning in late May.