The Limpopo River, which has burst its banks, is threatening the lives of residents in the Save River Valley, several hundred miles north of Maputo.
Widespread flooding in Botswana, Zimbabwe and parts of South Africa have been worsened following the arrival of Cyclone Eline which left more than 250 people dead in Mozambique alone.
Up to one million people now face risk of catching malaria and cholera.
The South African airforce which has been flying supplies by helicopter into the affected regions is on standby to airlift stranded residents along the banks of the Limpopo River.
Apart from Beit Bridge, all the border posts between South Africa, Zimbabwe, Botswana and Mozambique remained closed Sunday and there have been reports of vehicles swept away by the torrential rains in all four countries.
The busy town of Louis Trichardt in the Northern Province of South Africa was still cut off Sunday due to the flooding of the N1 highway which connects South Africa to Zimbabwe.
In Zimbabwe, a state of disaster has been declared in three of the worst hit provinces, and flood damage in South Africa's Northern Province - which has also been declared a disaster area - is likely to be more than 300 million US dollars.
At least 21 people have died in the province and emergency talks were underway Sunday afternoon to find ways to provide relief to the victims of the floods.
Graca Machel, the wife of former South African President Nelson Mandela, who toured some of the affected areas by helicopter Saturday, described the situation as devastating.
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