UN Office for the Coordination of Humanitarian Affairs spokeswoman Elisabeth Byrs said 500,000 people had been affected in West Africa and a further 500,000 in Sudan, and the numbers were rising.
Health charities have warned that many areas are in urgent need of food, shelter and medicine.
The BBC's Adam Mynott says not a single country in West, Central and East Africa has been unaffected by the torrential rain.
In Uganda, where at least nine people are reported to have died, government minister Musa Ecweru said the situation "borders a crisis".
"Several communities have been cut off and we cannot access them," he said.
In Ethiopia, one of the worst-hit east African nations, 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 particularly hard, with at least 20 people killed and about 400,000 people made homeless.
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.
Benonita Bismarck, from Ghana's Red Cross Society, said the situation was dire and cases of cholera have already been reported.
George Azi Amoo, co-ordinator of Ghana's disaster management body, said the floods had destroyed farmland, livestock and infrastructure.
"Some villages and communities have now been totally wiped off the map of Ghana," he told the BBC's Newshour.
In neighbouring Togo some 34,000 people have been displaced, at least 20 killed and the infrastructure has suffered major damage.
Officials in northern Rwanda said 15 people had died there and 500 homes had been destroyed since Wednesday.
Dozens are also reported dead in Sudan, which has been suffering some of the worst floods in living memory.
Kenyan government spokesman Alfred Mutua told the AFP news agency: "We have activated our disaster response and the government and aid groups are providing food, shelter and medicine to those affected by the floods."
Niger, Nigeria, Liberia, Mali and Burkino Faso are among other countries affected.
The BBC's Mary Harper says there is growing concern that unless emergency assistance reaches people quickly, they will become increasingly vulnerable to waterborne diseases.
UN Office for the Coordination of Humanitarian Affairs spokeswoman Elisabeth Byrs also warned that conditions were "ripe for an infestation" of locusts.
Last Mod: 16 Eylül 2007, 12:19