The death toll from flooding in eastern parts of South Africa has risen to 49, including four children on a school bus that was swept away, a provincial governor said on Wednesday.

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 taxi 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. (AFP)