More storms are forecast in areas around the Zambezi valley, where tens of thousands of people have been displaced by flooding.
Across the region the heaviest rains for almost a decade are forcing people to flee their homes, even as they try to recover from last year's floods.
The authorities in Mozambique are preparing to help up to 200,000 people.
Many remain trapped on islands in the Zambezi or have retreated to shrinking patches of high ground near villages.
Aid workers say the situation is getting worse, and meteorologists have forecast more storms for Zambia, Zimbabwe, Malawi and Mozambique.
"The soil is already saturated (with) water and the run-off is very high, an amount of water can cause massive devastation," said Mussa Mustafa, head of Mozambique's National Meteorology Institute.
Authorities say that over the weekend they will have to significantly increase the flow from the huge Cohara Bassa dam in western Mozambique to avoid the risk that it bursts.
That could create further problems for those displaced by the floodwaters, the BBC's Peter Greste reports from Caia in Mozambique.
It is only the beginning of the rainy season but the Zambezi is already well over six metres (20ft) deep - rapidly approaching the 7.6 metre (25ft) level that it reached during disastrous floods in 2000, he says.
In 2000, half a million people were forced to flee.
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.
In Mozambique, six people are known to have died - four drowned and two were killed by crocodiles.
Working with soldiers and international relief agencies, Mozambique's National Institute of Disaster Management has used boats and helicopters to move tens of thousands of people to temporary accommodation centres away from the flooding.
A further 14,000 people will be evacuated from the northern bank of the Zambezi on Saturday as water levels keep rising, the head of the institute told Reuters.
Thousands of people in the region have been displaced
Villagers have described climbing trees and running to higher ground to escape the floodwaters.
Some 27,000 people face food shortages in the affected areas, according to Radio Mozambique.
Rains have swamped city of Tete in the north of the country forcing some factories and schools to shut down, Reuters reported.
In Zambia, the 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 and 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.
The Malawian government is warning people to relocate from flood-prone areas, but many have been reluctant to leave their farms.
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