The death toll is the highest since 1998, when more than 4,000 people died, while damages from the ongoing disaster have been estimated in the tens of billions of dollars.
The rising flood waters have begun to test the limits of the Three Gorges Dam, the largest in the world spanning China’s longest river, the Yangtze.
Huge amounts of water thundered out of its massive spill-gates on Friday as the government of Jiangxi said the eastern province downstream was at a "critical juncture" in flood control.
"The dam's flood control capacity is not unlimited"
China Three Gorges Corporation official
The provincial ordered authorities to redouble flood prevention work along dozens of lakes and rivers already swollen by weeks of heavy rains.
"Over the next 20 to 30 days, the high water level of the Yangtze River's Jiujiang section and Poyang Lake will continue. The flood situation is very grim," the provincial government said in a statement.
With a wall running over two kilometres wide and 185 metres tall, it was built at a cost of $27bn.
The reservoir behind the dam holds around 39 trillion litres of water, but it is now reaching its limit with floodwaters sitting just 16 metres below the dam's maximum capacity, according to the state-run Xinhua news agency.
Already authorities have been forced the close the massive shipping locks built into the dam.
Zhao Yunfa, the deputy director of the China Three Gorges Corporation's dispatch centre, said this week that the dam's capacity can only withstand floods that reach up to 83,700 cubic metres per second - only about 18 per cent more than the dam's record water flow on Tuesday, the China Daily newspaper reported.
"The dam's flood control capacity is not unlimited," the newspaper quoted Zhao as saying.
The Hubei provincial government said several flood-hit areas had been put on "super-alert" in anticipation of increased water flow and the large Danjiangkou reservoir had reached its flood-control maximum.
|The massive shipping locks on the Three Gorges Dam have been closed [EPA]
Chen Lei, the minister of water resources, urged those responsible to continue to inspect and protect dams and reservoirs as well as prepare for heavy rainfalls.
Work teams have been dispatched to areas including Sichuan, Shaanxi and Gansu to co-ordinate flood-fighting efforts, Xinhua said.
Elsewhere in southern China, Guangdong province was hit by the full force of Typhoon Chanthu, the second such storm to hit the country in less than a week.
Chanthu made landfall late on Thursday with winds of up to 126 kilometres per hour sending debris flying through the air and killing at least two people.
State television broadcast images of large waves crashing onto the Guangdong shore and said electricity, telecommunications and water services were cut in some areas.
On Friday, Chanthu was downgraded to a tropical storm as it headed toward the city of Nanning, although it is still causing heavy rains.
Liu Ning, the vice-minister of water resources, warned of more misery to come as the typhoon season gets into gear, saying six to eight major typhoons were expected in the coming months.
Melissa Chan, Al Jazeera's correspondent in Jiangxi province, said while floods are an annual occurrence in parts of China, what is particularly unusual about these floods is that heavy rain has hit most of the country.
"The big problem now is that there is a storm brewing down south and when it moves northward it's going to bring more rainfall," she said.
"This rain keeps coming and coming and coming. When waters recede a little bit more rainfall comes."
Already, three-quarters of China's provinces have been plagued by flooding and 25 rivers have seen record-high water levels, officials said.
Qinghui Gu from the International Federation of the Red Cross in Hubei province, told Al Jazeera they were concerned about the availability of food, water and shelter for the next few months.
"There are over 300,000 people being evacuated from this area alone," Gu said.
"A lot of farmland has been flooded and completely destroyed. More rain is expected and a lot of small reservoirs have burst."