Nine people died in the southwestern Guizhou Province while another nine have been reported missing. More than 65,000 people have been relocated due to heavy rainfall and landslides this month, the ministry said in a statement.
Hailstorms have forced nearly 4,000 residents to relocate temporarily earlier this month and damaged over 520 hectares of crops in the province.
In the central Hunan Province, four persons died, six remained missing and 157,000 people have been evacuated.
The central government has dispatched emergency response teams to supervise relief work in the three provinces, state-run Xinhua news agency reported.
"The rescue and relief work in three provinces is going well," the statement said.
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.