Torrential rain has flooded massive tracts of land in 14 African countries in recent weeks, affecting about a million people, UN officials say.

The United Nations Office for the Co-ordination of Humanitarian Affairs (OCHA) says 500,000 people are facing hardship because of flooding in West Africa, while roughly the same number of people in central and eastern countries need relief aid to help them cope.

Sudan is one of the worst affected countries. Runoff waters from 10 per cent of Africa's land mass funnel down through southern Sudan and into the Nile River.

Flooding has left several hundred thousand homeless and 64 people dead in southern Sudan, the UN says.

Water-borne diseases like cholera are adding new perils to the misery. A cholera epidemic spread by floods is blamed in the deaths of at least 49 Sudanese in recent weeks, according to the World Health Organization.

At least nine deaths have been reported in eastern Uganda, where the UN says rainfall since July has been the heaviest in 35 years.

In Rwanda, 15 people have died from flooding since Wednesday, according to the agency.

The British Broadcasting Corporation reported on Saturday that not a single country in West, Central and East Africa has been unaffected by the torrential rain.

There are also been reports of flood-related deaths or homeless people in Burkina Faso, Togo and Ghana, as well as Ethiopia, Niger, Nigeria, Liberia, Chad, Senegal, Kenya and Mali.