Thousands of people were left destitute after heavy wind and rains battered the country's most impoverished region at the beginning of the week.

President Cyril Ramaphosa on Friday said the "catastrophic disaster" was due to climate change and estimated the flood waters had reached more than four metres (13 feet) high.

"The latest report has indicated an increase in the number of fatalities from 88 to 90," the Eastern Cape government said in a statement.

Thirty of the victims were children, it said.

Among them were at least six children who were on a school bus that was swept away in the flood. Three students were rescued after clinging to trees.

"About 2,686 residents were left homeless" and were accommodated in temporary shelters, the local government said.

The area worst hit by the floods and subsequent landslides was the city of Mthatha, about 800 kilometres (500 miles) south of Johannesburg.

The city is near the village of Qunu, birthplace of Nelson Mandela, the late anti-apartheid hero and former president.

Thousands of houses, roads, schools and health facilities were left caked in mud after being completely submerged in floodwaters.

Some people managed to escape to their roofs but others became stuck inside their homes when the water rushed in during the night.

Snow and heavy rainfall are common during winter in South Africa but coastal parts of the country were affected by "unprecedented" weather conditions, Ramaphosa said last week.

According to the Green Climate Fund, the country is highly vulnerable to the impact of climate variability and change, which increases the frequency and severity of extreme weather.