Millions of children will suffer disproportionately from the failed harvests and devastated livelihoods left behind by the El Nino weather phenomenon, Save the Children warned Tuesday.

El Nino affects rainfall patterns and causes both drought and flooding. As it recedes the Pacific cooling trend known as La Nina is set to begin.

"Children face protection risks as families and communities move in search of work, food, water and grazing land for animals," said David Wright, the charity's East and Southern Africa Regional Director.

The charity estimated that 26.5 million children could face malnutrition, water shortages and disease in affected African regions.

"Children are also finding it difficult to stay in school, due to hunger or lack of water," Wright added in a statement.

The 2015-2016 El Nino, one of the most powerful on record, has caused significant damage across several east and southern African countries, sending hunger levels spiralling and leading to greater spread of diseases.

Ethiopia has been experiencing its worst drought in 50 years, while Zimbabwe, Malawi and Mozambique all issued drought alerts earlier in 2016.

Despite African governments' best efforts the "sheer scale" of El Nino this time had outdone the states' capacity to deal with the crisis, according to Save the Children.

But the worst could be yet to come, Wright said, with the threat of La Nina further destabilising affected communities.

"The full force will be felt over the coming months," he said, announcing a humanitarian appeal launched by The South African Development Community (SADC).

Three UN bodies estimated in early July that about 40 million people in east and southern Africa would not have enough food in the aftermath of El Nino.