The death toll from flooding on South Africa's east coast has risen to 259 people, a provincial government official has said.

Homes have been ravaged and roads swept away by mudslides in Durban, a coastal city in the east of the country after intensely heavy rainfall began on Tuesday.

The new death toll revises an earlier estimate of just over 50.

President Cyril Ramaphosa has pledged to help the victims and has been visiting families who lost loved ones in the KwaZulu-Natal province - including a family with four children.

Africa's southeastern coast is on the front line of seaborne weather systems that scientists believe global warming is making nastier - and predict will get far worse in decades to come.

"You're not alone...We'll do everything in our power to see how we can help," Ramaphosa said. "Even though your hearts are in pain, we're here for you."

The flooding has disrupted shipping in one of South Africa's busiest ports.

The country's neighbour, Mozambique, has suffered a series of devastating floods over the past decade, including one last month that killed more than 50 people.

A report by the Intergovernmental Panel on Climate Change (IPCC) in February warned that humanity was far from ready even for the climate change that is already baked into the system by decades of fossil fuel-burning and deforestation.

It urged the world to ramp up investments in adaptation.

South African pulp and paper maker Sappi said on Wednesday its staff were unable to travel to work due to the flooding and that the transport of goods had been disrupted, impacting three mills.

South Africa's biggest logistics and freight operator Transnet, which runs the port of Durban, gradually resumed operations there on Wednesday after suspending them on Tuesday, the public enterprises ministry said.