"The reasons for this serious situation are many, but there are three main areas that have not been brought under effective control -- waste water discharge in cities, industrial effluent and agricultural pollution," he said.
Per capita water resources in the world's most populous country are less than a third of the global average, and falling.
A drought this summer in southwestern China's Chongqing city and Sichuan province has left more than 18 million people short of drinking water -- greater than the population of the Netherlands.
In China's rapidly growing cities, where people from the much poorer countryside have flocked in the last few decades, hoping to share in the country's economic growth, almost half of all waste water is simply dumped untreated into rivers and lakes.
Leaky pipes and over-use of groundwater have exacerbated the situation, he added, and have even led to severe subsidence problems in some cities.Northern China, where a third of the country's population lives, also suffers from increasingly dry conditions, the official said, reducing the amount of water available.
Qiu said the government would spend more than 1 trillion yuan (US$125.5 billion) in the next five years on new sewage works, pipes, desalinisation plants and projects like the massive South-North water diversion scheme.
"We are standing at a crossroads," said Qiu, who admitted to only using bottled water to make tea because of poor tap water quality in Beijing.
Conservation efforts in some cities including Beijing, which is preparing for a self-styled "green" Olympics in 2008, have helped cut water consumption. Zhang Yue, deputy head of the ministry's urban construction department, said Beijing used 500 million tonnes less water in 2005 than in previous years.
But Qiu said that raising low water prices to promote conservation was not an easy option. He said that water costs of US$5 a tonne as in Boston, or 2.5 euros a tonne in France, would not work in China.