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Other parts of the country have also been hit by flash floods
"What happened this year can only be matched by what happened 40 years ago," Mr Machar told the BBC after touring the flood-affected areas.
At least 10,000 people are affected and six of South Sudan's 10 states have been declared a disaster zone.
Thousands have been returning to South Sudan after a 2005 peace deal ended a long civil war between north and south.
Mr Machar said he had done an aerial survey of counties in Upper Nile and Unity States.
"The situation was desperate in Unity State, where I saw a whole county displaced by the floods," he told the BBC's Network Africa programme.
In Upper Nile's more urbanised Renk county he said the water plant had been polluted and 4,000 people were desperately in need of water and shelter.
"We're afraid disease will spread," he said.
The United Nations and various aid agencies are distributing food and drugs, but he said there was a need for more aid - especially shelter.
"The houses have collapsed because they're weak structures," Mr Machar said.
At least two people have died in the floods in the south and at least 41 in flash floods across the country during this rainy season.
The capital, Khartoum, where the White and Blue Nile meet, is bracing itself for more rising water.The AP news agency reports that products such as mosquito nets have doubled in priced as city residents fear a malaria outbreak that often comes with floods.
Story from BBC NEWS:
Published: 2007/07/31 15:06:42 GMT
? BBC MMVI
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