Some 50,000 people in Mozambique have been displaced by flooding along the Zambezi valley, authorities say.
They say between 150,000 and 200,000 people could be affected over the coming weeks if forecast rains fall in upper reaches of the valley.
The Zambezi has already burst its banks in some areas forcing tens of thousands of people to flee their homes.
Villagers have described climbing trees and running to higher ground to escape the floodwaters.
And the river is continuing to rise.
Antonio, a villager in Sofala in central Mozambique said the effect of the rains had been terrible.
"People had to climb trees and run to high ground," he told Reuters news agency. "People don't have anywhere to go - we just hope help will come."
January is usually the middle of the wet season for southern Africa but is rarely as wet as this, says the BBC's Peter Greste in central Mozambique.
Across northern Zimbabwe, southern Zambia, Malawi and Mozambique, relentless rain has waterlogged fields, destroyed fields and washed out roads and villages.
Damage to crops and roads has raised fears of food shortages, and aid agencies have also warned of increased risk of waterborne diseases and diseases caused by poor sanitation.
The Zambian government has appealed for $13m (£6.6m) in foreign aid to help deal with the effects of flooding, which officials say has displaced thousands of people.
Zambia's head of disaster management, Austin Sichinga, said that the heavy rains had also caused extensive damage to infrastructure.
In low-lying areas of Zimbabwe, flooding has destroyed homes, livestock and infrastructure, aid agencies report.
Heavy floods have also destroyed homes and crops, displacing thousands of people in southern and central Malawi, reports the BBC's Raphael Tenthani in Blantyre.
The Malawian government is warning people to relocate from flood-prone areas, but many are reluctant to leave their farms, our correspondent reports.
In Mozambique, where floodwaters have reached a depth of 6m in some areas, six people are known to have died - four drowned and two were killed by crocodiles.
Some 27,000 people face food shortages in the affected areas, Radio Mozambique reports.
More to come
And the worry is that the worst may not be over.
This is because rain falling in the upper catchments area of the Zambezi has not yet travelled downstream.
Thousands of people in the region have been displaced
There is still the risk of another surge as water from rainfall upstream flows though the Zambezi River valley in the centre of the country, our correspondent says.
The UN resident coordinator for Mozambique, Ndolam Ngokwe, told the BBC that 50,000 people had been evacuated to resettlement centres and the numbers were expected to increase.
Mozambique's National Institute of Disaster Management has been co-ordinating the emergency response.
Working with soldiers and international relief agencies, it has used boats and helicopters to move people to temporary accommodation centres away from the river.
Its director, Paulo Zucula, says that if forecast rains fall in the catchment area, the Zambezi could reach levels as high as in 2000. Then, half a million people fled the rising water.
A further 14,000 people will be evacuated from the northern bank of the Zambezi on Saturday as water levels keep rising, Mr Zucula told Reuters.
"Two or three resettlement areas may not be safe. Property and infrastructure is now being wrecked but we are worried about the people," Mr Zucula said.