The report says billions of tons of waste are dumped into the river every year with excessive levels of ammonia, nitrogen and phosphorous taking a huge toll.
The study by the Chinese Academy of Sciences, the WWF and the Yangtze river Water Resources Commission is the first annual health report on the state of the Yangtze.
"It's a pressing job to regulate such activities in all the Yangtze drainage areas and promote harmonious development of man and nature," Yang said.
According to the report's authors, cities along the 6,211km-long Yangtze annually dump at least 26 billion tonnes of waste water into the river, which accounts for just over a third of China's fresh water resources.
Rare species such as the the baiji dolphin are believed to have been driven to extinction by pollution, while common species such as the carp are not far behind, the report warned.
Li Lifeng, the freshwater programme director of the World Wide Fund for Nature (WWF) China, said: "A direct result of pollution is shrinking fish catch."
According to the study the river's annual harvest of aquatic products dropped from 427,000 tonnes in the 1950s to about 100,000 tonnes in the 1990s.
It also said the Three Gorges Dam reservoir, the world's largest water storage facility, had become badly polluted by pesticides, fertilizers and sewage from passenger boats.
Last month Wen Jiabao, the Chinese premier, told the opening session of the National People's Congress that the goals of China's economic growth needed to be balanced with protection of the environment.
|Cities along the Yangtze annually dump billions of tonnes |
of waste water into the world's third-longest river [Reuters]