Seven people died in flooding caused by severe winter weather lashing eastern areas of South Africa and school children are missing after a minibus was swept away, the government said on Tuesday.

Three children were rescued after spending hours in trees to escape rising waters near the Eastern Cape city of Mthatha, one of the areas hardest hit by the storm that struck on Monday, the provincial government said in a statement.

Six bodies were found in the city, which is about 800 kilometres south of Johannesburg, and a seventh body was found near a river in the rural Tsolo area, the statement read.

"The search is still ongoing regarding a minibus carrying school children that swept away earlier this morning," the provincial government said, without giving details on how many were onboard.

Disaster management teams

The province said it had deployed disaster management teams to assist people affected by the severe cold front, which also brought snowfalls to several areas.

Local media reports said residents of Mthatha had been trapped on rooftops in bitterly cold conditions early on Tuesday.

Around 200 people had taken shelter in a community hall in the town of Butterworth, about 110 kilometres away, after their homes in an informal settlement were flooded, reports said.