"This year they harvested nothing," said the World Food Programme's executive director Cindy McCain, after meeting farming families.
The drought has obliterated crops in Zambia, the epicentre of the crisis, where 70 percent of the population relies on agriculture to survive.
Combined with the other countries in the region, "we have a humanitarian catastrophe", McCain said, pleading for global support.
Last month Zambia's President Hakainde Hichilema appealed for almost $900 million to help counter the worst dry spell in the country's history.
According to the WFP, $409 million is needed for the first six months to assist some 48 million people in Malawi, Zambia and Zimbabwe.
The three countries, which have declared a state of national disaster, saw 40 to 80 percent of their maize harvest destroyed.
Grain shortages exacerbate food insecurity in the region where maize accounts for almost 20 percent of calories consumed.
The El Nino phenomenon is caused by the large-scale warming of surface temperatures in the central and eastern equatorial Pacific Ocean.
It occurs on average every two to seven years, leading to hotter weather globally.
The current El Nino emerged in mid-2023 with episodes typically lasting nine to 12 months.
The food agency said extreme climate conditions were a reminder of the urgent need for investment in activities that build resilience in southern Africa.
"Although this El Nino cycle is coming to an end, the impact of extreme drought will have tragic consequences for months to come," the WFP said.
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