The worst floods in three decades have now affected 22 countries, displacing hundreds of thousands and starkly raising the risk of epidemics since the deluge hit parts of the continent in July.
The worst-hit country since unprecedented downpours swept across the continent in August has been conflict-wracked Sudan, where the United Nations said up to 625,000 people could be in need of emergency aid.
VIDEO: Flooding exacerbates food shortages
The World Food Programme says it would begin airdrops of food next month in areas cut off by the severe flooding.
Africa's largest country has been hit by several waves of torrential rainfall in different regions and the floods have worsened a cholera outbreak that has already caused 68 deaths.
"At least 100,000 additional people have been directly affected by the latest wave of flooding in Sudan, which has destroyed homes, as well as food stocks and essential household supplies," the UN said in a statement.
In neighbouring Uganda, at least 400,000 people are awaiting relief in north-eastern regions where flooding has complicated aid delivery.
Fresh rain in western Ethiopia has brought renewed flooding to the town of Gambella and its region, said UN humanitarian coordination office spokeswoman Elisabeth Byrs, raising the number of affected Ethiopians to 226,000.
In Niger, at least seven people have been killed and more than 57,000 others affected by the heavy downpour since July.
At the weekend, 12 Central African Republic soldiers returning from a patrol drowned while crossing a swollen river, the defence ministry said yesterday.
Food crisis looms
Donors have scrambled to avert what aid agencies have warned could evolve into a deadlier crisis causing long-term food shortages in some of the world's poorest countries.
The United States announced on Monday that it already allocated $500,000 dollars ($A570,000) in contributions to the relief effort in Uganda.
"The cumulative effects of the rainfall have begun to compromise the structural integrity of many dirt homes, contaminate wells, inundate latrines, and wash away seeds," the US agency for international development (USAID) said.
The European Union and several other countries have pledged millions to fight the crisis.
The UN Food and Agriculture Organisation pledged Tuesday to use all its resources to help the flood-hit countries which will cost around 12 million dollars.
La Nina blamed
The disaster crippled the continent even as world leaders discussed climate change at the United Nations General Assembly in New York.
The torrential rains and floods that have ravaged sub-Saharan Africa are believed by some experts to be caused by the "La Nina" weather pattern, thousands of miles away in the Pacific Ocean.
Several government officials have warned that the floods were a wake-up call for the world, and especially the poorest countries, to increase their preparedness for disasters induced by climate change.
The floods caught governments and aid agencies off guard, as heavy rains are common in August and September in many of the affected countries.
Kenya announced Monday it would spend $US97 million ($A110 million) to bolster flood defences in the west of the country, where at least 15 people have died as a result of the floods since August.
In Ghana, one of the worst hit countries on the Atlantic coast, some 140,000 people were made homeless.
The inaccessability of many areas makes it difficult to assess the human cost of the floods, but figures based on reports by hospital, government and humanitarian sources put the toll above 300.
The latest update came Monday from Burkina Faso, where the government said at least 33 people have died since August.
Aid agencies have launched appeals for emergency funds to counter the effects of the flooding and prepare for its aftermath.