The storms have dumped more than 20 centimetres of rainfall in 48 hours on some towns, toppled thousands of homes, and dislocated tens of thousands of residents, the ministry said yesterday.
The deaths were caused by house collapses, landslides, drowning or lightning.
Hubei province, where heaviest rainfalls were recorded, reported the highest death toll of 10. The local civil affairs agency said 664,000 people were affected.
In the neighbouring province of Hunan, the storms affected 527,000 people.