In the east of the continent, Ethiopia, Rwanda and Uganda are the worst hit countries, with at least 87 people dead. Sudan, Kenya and Rwanda have also been affected.
After days of heavy rain, tributaries that flow into the Nile have burst their banks, flooding villages in Uganda's Lira district.
The heaviest rainfall in 35 years has displaced at least 150,000 people in eastern Uganda, and, according to authorities, the rain has been "worsening by the hour".
Crops destroyed
Rising flood waters have resulted in as many as 400,000 people losing their livelihoods due to crops being destroyed, Musa Ecweri, the state minister for relief and disaster preparedness, said.
Nine peope died after being washed away by floodwater or struck by lightning during violent storms.
Ecweru said the death toll was expected to rise, with rain still falling across large areas of the region.
Niels Scott, from the International Federation for the Red Cross in Geneva, told Al Jazeera: "We've already started... to provide shelter equipment, mosquito nets and tarpaulin.
"Many of them have lost their houses... they've lost grain stores, they've lost their livelihoods.
"They're looking at a very grim six months. They've got the immediate future to worry about and then they've... got to prepare for the next growing season."
Landslides
Aid organisations have stepped up efforts to get food and clean water to villagers, but landslides triggered by additional rainfall have washed away roads and aid access is currently limited, officials said.
Gilbert Buzu of the World Food Programme, said: "You will find water flowing over the bridge and in some areas people are using dugout boats to cross the bridge and, of course, that makes it very impossible for the trucks to move through."
The UN is expected to send helicopters and boats to boost relief efforts.
Ethiopia, Rwanda and Sudan are also affected, with hundreds of thousands now at risk of water-borne disease.
Ghana floods
In West Africa, 12 countries are flood-affected, with Ghana and Nigeria sustaining the heaviest damage.
Eighteen people are reported to have been killed after floods hit dozens of villages in northern Ghana.
Local residents said the death toll may rise further.
More than 250,000 people have reportedly lost their houses in the floods.