Major disruptions are being reported at Durban and Richards Bay amid unrest following the jailing of former South African President Jacob Zuma.
The South African Association of Freight Forwarders said the lack of health services at Durban, the country's principal port, had been effectively preventing vessels from berting due to lack of Covid-19 testing, Reuters reported.
Meanwhile, state-owned logistics outfit Transnet told the newswire that "the entire supply chain is closed" there and at Richards Bay, including roads into and out of the ports.
AP Moller-Maersk has also shut down its depots, warehouses and cold stores in Durban and Johannesburg as protests in the cities turned to looting.
"The port of Durban has had many of the terminals shut over the last 24 hours, however at this stage we have not triggered any contingencies that will cause ships not to call at Durban," Maersk's Africa spokeswoman Kerry Rosser told Reuters.
The company said on Monday that it would be not be invoicing detention charges to customers until 19 July, with some depots shuttered and others working with a skeleton crew.
"[The unrest] represents a serious threat to our lives and livelihoods," the company said in an advisory.
By Wednesday, media reports said 72 had died in the unrest, including 10 in a stampede, as shopping malls and warehouses were ransacked and set on fire.
The BBC cited South African police saying they had arrested 1,234 people in connection with the riots and identified 12 as allegedly having provoked the unrest.
Durban and Johannesburg have reportedly borne the brunt of the unrest, with traffic on the highway connecting the two cities interrupted.
Zuma, who served as president from 2009 until his resignation in 2018, was sentenced to 15 months in prison on 29 June for contempt of court after failing to appear before a government commission investigating alleged corruption during his administration.
He was arrested the next week.
Reuters cited statements from Zuma's foundation blaming the violence on his imprisonment, with a spokesperson from the group saying the violence could have been avoided if Zuma was not arrested.
