Ministry of Civil Affairs statistics show the three provinces in the valley -- Anhui, Jiangsu and Henan -- have suffered economic losses of nearly 7.2 billion yuan (871 million US dollars).
Most of the destruction has been in central China's Anhui province, where eight people have been killed and 18 million affected, said Wang Xintao, an official from the provincial civil affairs department.
"It's the worst flooding since 1991 in terms of the volume of rainfall and water level," Wang told AFP.
The official Xinhua news agency said more than 5,700 villages in Anhui are besieged by floodwaters.
Wang said 378,900 people living in the flood valley have been relocated to higher ground, but even highlands were surrounded by water, leaving 1.14 million residents there stranded.
They were not under immediate danger, but many of them were living in tents distributed by disaster relief officials.
"The military will send a boat out to deliver necessary foods and daily necessities to them," Wang said.
Severe damage was also inflicted on farmland, with more than one million hectares ruined.
Agricultural damage alone is estimated to be 3.4 billion yuan.
A provincial flood control official told AFP Monday more than 5,000 people had been injured or become ill in the floods.
To tackle the problem, the ministry has allocated 37 million yuan of disaster relief funds to Anhui and sent 11,000 tents to Anhui and Jiangsu.
Flood waters also brought death and destruction to the central province of Henan, further upstream along the Huai, one of China's major rivers which is highly flood-prone each summer.
So far, two people have died there, with five million affected, according to an official with Henan's department of civil affairs.
The official said 110,000 people have been relocated.
Direct economic loss to the province is one billion yuan, and 60,000 hectares of farmland have lost their harvest.
No casualties have been reported in Jiangsu, but over 13 million people are affected and 710,000 hectares of farmland ruined, Xinhua said.
Local rescue teams have been working to provide food, potable water and accommodation for victims.
Flooding also snarled rail and road traffic in the region as sections of railway lines in Anhui collapsed and flooded, leaving tens of thousands of passengers stranded, the China Daily said.
In Shanghai, all cargo trains have been stopped and five passenger service trains are still unavailable.
In Nanjing, 10,000 railway passengers were delayed when floods halted operation on 16 trains, the report said. The railway has yet to be repaired, and more trains could stop operating.
A state of emergency was declared at midnight Friday in the region where, according to the weather service, rain will continue for several days.
China's flood season usually starts around June and heavy rains are affecting large swathes of the country.
Earlier this month, official media said rains in the south of the country had left at least 148 people dead and affected 45 million.