The State Flood Control and Drought Prevention office reports floods this year have already killed at least 823 people, left 437 missing and caused tens of billions of dollars in damage.
It said two dozen major rivers had risen beyond their warning levels.
The water level in the massive Three Gorges Dam, the world's largest hydroelectric and flood control project, hit its highest level ever last week.
More torrential rains are expected for the southwest, southeast and northeast.