The UN is warning of fresh rains and outbreaks of water-borne disease across Africa, where flash floods have already affected more than one million people.
Scores of people have died and hundreds of thousands have been displaced by the floods that have submerged much of the continent's most productive farmland.
The UN said there was an urgent need for food, shelter and medicine.
At least 14 countries have been hit in West, Central and East Africa by some of the worst rains in living memory.
UN spokeswoman Elisabeth Byrs said: "The rains are set to continue and we are really concerned because a lot of people are homeless and infectious diseases could emerge."
"We have 500,000 people affected in 12 countries in West Africa, and also in East Africa - in Sudan and Ethiopia.
"Some of the poorest countries, like Mali, Burkina Faso and Niger - the poorest nation in the world - are badly affected," Ms Brys told the BBC.
The UN said the floods could lead to locust infestations and outbreaks of water-borne diseases such as cholera and dysentery.
One of the worst-hit areas is Uganda, where up to 400,000 people have been affected by the country's heaviest rains for 35 years.
At least nine people are reported to have died, and government minister Musa Ecweru said the situation "borders a crisis".
The BBC's Sarah Grainger arrived in Magoro in Katakwi district by helicopter. She described inundated roads and fields and said people were using dug-out canoes to move around.
She says many of the 7,000 inhabitants have lost their crops and food security is now one of the biggest issues.
The airlifting of food and medical supplies to affected areas is expected to start on Monday or Tuesday. The UN has diverted a helicopter from Darfur in Sudan to help with the effort.
In Ethiopia, deaths have been reported and a massive food aid programme has been set up after flooding hit almost 200,000 people.
In West Africa, Ghana has been hit hard, with at least 20 people killed and about 400,000 people made homeless.
Sudan has seen some of its worst floods in living memory
The floods have submerged land which produces food for the entire country. President John Kufuor has declared the north of his country a disaster zone.
George Azi Amoo, co-ordinator of Ghana's disaster management body, told the BBC: "Some villages and communities have now been totally wiped off the map of Ghana."
He said food and clothing were being distributed, and that the navy had sent two boats to help ferry people to safety.
In neighbouring Togo some 34,000 people have been displaced and the infrastructure has suffered major damage after rains demolished 100 bridges and seven dams.
Dozens are also reported dead in Sudan, which has suffered some of the worst floods in living memory. The death toll may rise as much of the affected area is inaccessible except by air.
Officials in northern Rwanda said 15 people had died there and 500 homes had been destroyed since Wednesday.