Torrential rains and freezing temperatures struck the largely rural and underdeveloped Eastern Cape on Monday, causing major flooding that submerged houses and swept away at least one minibus transporting children to school, four of whom were still missing.

"We may have more people unaccounted for," Eastern Cape government spokesperson Khuselwa Rantjie told AFP.

Rantjie said that five teams were involved in search and rescue efforts around the city of Mthatha, about 800 kilometres (500 miles) south of Johannesburg.

Among the 49 confirmed dead, at least four were children, the province's top official, Lubabalo Oscar Mabuyane, said on Wednesday.

They had been in a school minibus carrying 11 children that was swept away by high water.

Authorities said four children and two adults in the bus were confirmed to have died, while three children were found alive.

"We have never seen this kind of combination of snow and torrential rains in winter simultaneously," Mabuyane said.

"We are reeling," Basic Education Minister Siviwe Gwarube told public broadcaster SABC News in an interview from Mthatha early Thursday.

She said that in addition to the schoolgoers in the minibus, a boy died when he was swept away by water while walking to school.

Images on local media showed houses completely under water and rescue teams wading through the mud.

Around 600 people have been displaced, the provincial government said, with many sheltering in community halls.

There was also significant damage to infrastructure, including to power and water supplies, with at least 20 health facilities affected, local authorities said.

The province, where Nelson Mandela was born, is among the poorest in the country, with 72 percent of its population living below the poverty line, according to the Southern African Regional Poverty Network.

President Cyril Ramaphosa said in a statement that emergency services, including the National Disaster Management Centre, were "giving the requisite attention to crises as they unfold".

Snow and heavy rainfall are common during winter in South Africa but the country is also highly vulnerable to the impacts of climate variability and change, which increases the frequency and severity of droughts, floods and wildfires, according to the Green Climate Fund.