El Nino, a natural weather pattern linked to extreme droughts, storms and floods, could be one of the strongest on record this year. Parts of Africa are already facing hunger, disease and water shortages.
El Nino, which is sparked by a rise in sea surface temperatures in the equatorial Pacific, has caused drought in several parts of Africa.
The worst affected country is Ethiopia, which is suffering its severest drought in 30 years.
Ethiopia has a population of 90 million of which eight million need food aid. That figure could rise to 15 million by early 2016, the United Nations says, as failed rains during both the spring and summer have created food and water shortages.
The Ethiopian government has said it would start distributing 222,000 tonnes of wheat this month and plans to import almost double that amount if the scale of the food shortage does not diminish.
The government and aid agencies say Ethiopia needs $600 million to cope with the crisis.
In South Africa, a devastating drought - the worst since 1982 - is claiming thousands of livestock in North West province.
Lardus van Zyl, chairman of the Red Meat Producers Organization, told AFP that farmers were auctioning their stocks before they die and nearly a third more animals were being butchered compared to the same period last years "mainly because of the drought."
El Nino originates in the eastern Pacific Ocean but has an impact in many parts of the world
South Africa's agriculture minister Senzeni Zokwana has warned of "regional disaster" if the drought persists.
Governments say they are prepared
El Nino causes scorching weather in some regions and heavy rains and flooding in others.
Such extremes can occur in the same country. DW's Mirriam Kaliza says floods, dry spells and drought are expected in some parts of Malawi, according to the local department of climate change. Malawi's Department of Disaster Management and Preparedness has been assuring citizens it is prepared for El Nino.
In Uganda, droughts have been also followed by heavy rains. DW's Alex Gitta in Kampala says the government is appealing to families living in mountainous areas threatened by landslides to move elsewhere. It was also training army and police personnel in disaster management.
Aid agencies hope El Nino will encourage governments to respond to public concern and take action on climate change
In Kenya, DW's James Shimanyula says torrential rains have killed 20 people in three weeks and floods have swept away homes, livestock, and thousands of acres of crops. But El Nino rains have also pounded Kenya's northeast which is normally very dry. Kenya was caught unawares by El Nino in the 1970s but is now better prepared, the authorities say.
The World Meteorological Organization (WMO) said the current El Nino was already "strong and mature" and the biggest in more than 15 years. It was already in the same league as those seen in 1972-73, '82-'83 and '97 to '98, the WMO said.
WMO Secretary General Michel Jarrud warned that this latest naturally occurring El Nino and human induced climate change may interact and modify each other in ways we have never been experienced before. "El Nino is turning up the heat even further," he said in a reference to the increase in global surface temperatures.
Aid agencies hope that the humanitarian crisis caused by the weather pattern will focus minds at the forthcoming UN climate talks in France at the end of November.
"It's intensity and potential destructiveness should be a wake-up call as world leaders gather in Paris," said Anthony Lake, executive director of UNICEF.