The downpours intensified last week, causing dozens of Yangtze-basin waterways to post record-high water levels, while more than 400 had exceeded warning levels.
"Since June, average precipitation in the Yangtze river basin has been the highest since 1961," said Vice Minister of Emergency Management Zheng Guoguang.
Concern was now shifting downstream to Poyang Lake, which drains into the Yangtze in hard-hit Jiangxi province and is the largest freshwater lake within China's borders.
State-run Xinhua news agency said water levels at a key hydrological station on the lake broke a record set in 1998, when more than 4,000 people were killed by floodwaters.
State media reported that more than 100,000 people, including rescue personnel, soldiers, and ordinary citizens, had been thrown into flood-control efforts in Jiangxi.
Around half of those were deployed at Poyang Lake, where many dikes and levees had collapsed.
In the city of Jiujiang, near where the lake drains into the Yangtze, soldiers wearing orange life vests fortified the river bank with a wall of sandbags piled as high as a man.
Summer rains and seasonal glacial melt in the river's Tibetan plateau causing routine annual flooding.
But environmentalists say the threat has worsened over the decades due in part to rampant construction of dams and levees that have cut connections between the river and adjacent lakes and floodplains that for centuries had helped absorb the summer surge.
Conservationists also warn that the rapid melting of Himalayan glaciers due to climate change may lead to more dangerous summer flooding.