The death toll after the severe winter storm struck on Monday was likely to rise and it was not even clear how many people were missing in the largely rural and underdeveloped province, they said.

"As of now, the stats have escalated to 49" deaths, Eastern Cape premier Lubabalo Oscar Mabuyane told reporters.

They included four children on a school minibus carrying 13 people that was swept away by a flood near the city of Mthatha, Mabuyane said.

"Sadly, four of those learners have been confirmed to be deceased, together with the driver and the conductor of the minibus taxi," he said.

"Four learners are still missing and are still being looked for."

Three others had been found alive, he said.

Much of South Africa has been struck by heavy rainfall and bitterly cold conditions in the past days, with snowfalls in several areas and strong winds causing damage.

The Eastern Cape, which stretches from the Indian Ocean into high inland mountains, has been particularly hard hit.

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

- 'Dead or alive'-

Authorities did not give details of the other victims of the disaster and said the situation was evolving.

"Now we are busy with the rescue operation. So we are trying to get figures, our people out of that situation, dead or alive," the premier said.

"What we would not know, besides the four kids, is to how many people are we looking for," provincial transport minister Xolile Nqatha told the same press conference, confirming the death toll of 49 was likely to increase.

Images from the remote area have shown informal settlements under water. On Tuesday, three children were rescued after spending hours in trees to escape rising waters, authorities said.

Hundreds of families were sheltering in community centres in the bitter cold. There had also been significant damage to infrastructure, including power and water supply, provincial officials said.

- Lack of resources -

Mabuyane told public broadcaster SABC News earlier that only one helicopter was available in the province.

"We need more resources," he said. "We have never experienced disasters like this but now it's inevitable with climate change and global warming."

President Cyril Ramaphosa said in a statement that harsh winter conditions "remain life-threatening" adding that emergency services, including the National Disaster Management Centre, were "giving the requisite attention to crises as they unfold".

South Africa's national weather service has warned that severe and extreme winter weather conditions would persist until at least the middle of this week.

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 drought, floods and wildfires, according to the Green Climate Fund.