Transnet, which manages South Africa's freight rail network and ports, declared force majeure last week after its workers went on strike over a wage dispute.
In an update on its website, Transnet Port Terminals said the strike had impacted waterside and landside operations at its Durban port, which handles 65% of South Africa's container volumes.
"Please be advised that operations at Pier 1, Pier 2 and Durban RoRo Terminal have been impacted as a result of industrial action. Appointment slots have been suspended. Please do not dispatch trucks to the terminals until further notice," it said.
Piers 1 and 2 are container terminals, while the RoRo (roll-on roll-off) terminal is used to import and export cars.
The strike could also disrupt fruit exports from Transnet's Cape Town port just as the deciduous fruit season begins.
"Transnet is working closely with industry to ensure that the perishable products, along with other cargo with a limited shelf-life, are prioritised at the ports," Transnet said.
The company said the impact of the strike differed across its operations, with essential services such as ship docking and berthing continuing. Services provided by private companies within the ports were also continuing, it said.
"The focus for Transnet management is to keep operations going with the limited resources available," it said in response to Reuters' questions.
The Transnet strike is also set to worsen the mining industry's logistics woes. Even before the strike, South Africa's Minerals Council had projected a revenue loss of 50 billion rand ($2.76 billion) this year, compared to 35 billion rand in 2021, as Transnet's underperformance squeezes exports.
Miners Thungela Resources, Kumba Iron Ore and Jupiter Mines have warned that the strike is likely to impact coal, iron ore and manganese production and exports.
Transnet has said it will meet union leaders on Wednesday to continue wage negotiations.
($1 = 18.0852 rand)
(Reporting by Nelson Banya, Editing by Helen Reid, David Evans and Jane Merriman)