Heavy rainfall, snow and cold winds have particularly affected areas of the Eastern Cape province, with most of the country experiencing brutal winter weather conditions since last week.

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

The dead included four children on a school minibus bus 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.

Mabuyane did not give details of the other victims of the severe winter storm and said the situation was evolving.

"Search and recovery operations are continuing across all affected areas," he said.

The torrential rains over recent days, which also caused landslides, had forced hundreds of families to leave their homes and "significant damage on critical infrastructures", he said.

On Tuesday, three children were rescued after spending hours in trees to escape rising waters, authorities said.

- Lack of resources -

Several hundred people had been displaced since Monday, mainly from OR Tambo and Amathole districts, with some moved to schools and town halls.

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 support from the National Disaster Management Centre, were "giving the requisite attention to crises as they unfold".

He called on South Africans "to display caution, care and cooperation as the worst impacts of winter weather take effect".

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.