The United Nations refugee agency said the new cycle of flooding was washing over the world's youngest country just as renewed conflict is threatening a fragile peace.

"South Sudan is once again experiencing some very severe flooding, and unfortunately mostly in parts of the country that have been hit by renewed fighting," Marie-Helene Verney, UNHCR's representative in South Sudan, told reporters in Geneva, speaking from the capital Juba.

In recent weeks, she said, rising waters had submerged vast areas in Jonglei, Upper Nile and Unity states.

"There's about 100,000 people who have been displaced," Verney said.

"If this trend continues, we're looking at more than one million people affected during the next few months, of (whom) 400,000 will be displaced," she warned.

That would exceed the numbers already displaced due to devastating flooding in South Sudan last year, she said.

The situation is particularly concerning, Verney stressed, "in a year when we are seeing really a very sharp increase in armed conflict, (and) where we are still tackling arrivals from Sudan", which is facing a brutal civil war and the world's worst humanitarian crisis, according to the UN.

A sharp reduction in foreign aid funding globally is also taking its toll.

"The response UNHCR and others can provide is clearly not what it should be," Verney said.

"In Unity State, which is 70 percent underwater, UNHCR has significantly scaled down operations due to the funding shortfall, leaving thousands of displaced people in a more precarious situation," she said.

The UN refugee agency is urgently appealing for more international support.

The agency has appealed for $300 million to provide assistance in South Sudan this year, but had only received a third of that amount by the end of July she said.