Hunan flood control authority said 1,826 houses were destroyed in storms in the northwestern and southeastern parts of the province. At least four large reservoirs opened gates to release water in Hunan.
Schools were closed in Jianghua County after several campuses were inundated, state-run Xinhua news agency reported.
A section of highway near Guidong County was made impassable by a landslide and local authorities estimate that it will take 20 days to clear up the debris.
Meteorologists said the floods are linked to the strong El Nino event, expected to come to an end later this month.
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The current weather front is similar to one that triggered heavy flooding of the Yangtze in 1998, which resulted in 1,320 fatalities.
The Yangtze, Huaihe and Xijiang rivers may see "quite large" floods this year due to unusually heavy rain, with the average national precipitation level second only to that in 1961, the State Flood Control and Drought Relief Headquarters said in a statement.
Warnings over potential geological disasters have also been issued. Rain will continue to the south of the Yangtze, along the Huaihe and in south China over the next three days, weather forecasters said today.
Another storm front will hit Sichuan and Shaanxi provinces and regions in the lower and middle reaches of the Yangtze between May 31 and June 2, the China Meteorological Administration said.