The El Nino conditions are the strongest since records collection began in 1951, and resemble a 1998 weather pattern that flooded the river and killed thousands, the official Xinhua news agency said on Friday, citing vice minister of water resources, Liu Ning.
"Precipitation in the upper, middle and lower reaches of the river is forecast to be as much as 80 percent more than normal from May to August," Xinhua said.
Some Yangtze tributaries had already begun flooding and the flood control and drought relief situation was "extremely severe", Liu said, according to the news agency.
Provinces and cities along the river needed to make contingency plans, Xinhua cited Wang Guosheng, the governor of central Hubei province, as saying.
China has frequently been devastated by natural disasters, particularly by floods and earthquakes that have claimed millions of lives over the centuries.
Flooding, an annual problem, has been exacerbated by urban sprawl and poor drainage infrastructure in many cities.
Xinhua said 1,320 people died in the 1998 floods, though estimates vary and some put the death toll at more than 4,000.
Floods could be a test of the water management capabilities of the controversial $59 billion Three Gorges Dam, which was finished in 2012. Along with power generation and navigation, the dam was designed for controlling the Yangtze's water levels.
The ongoing El Nino, a warming of sea-surface temperatures in the Pacific, has been linked to serious crop damage, forest fires and flash flood and drought around the world.
Experts have warned that changing global climate leading to extreme weather will likely have an impact on the world's most important commodity crops - maize, soybean, wheat and rice.
Most of the global production of these four crops comes from a small number of countries such as China, the United States and India.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)