The ban on passenger vessels and cruise liners will continue except for the Mossel Bay and Saldanha Bay ports when the country enters Level 3 lockdown on Monday.
On Saturday, Transport Minister Fikile Mbalula said there would be no changes to the directions regulating the movement of ships.
He added only vessels bringing in cargo were allowed to call on all ports.
Mbalula said only full operations at the Mossel Bay and Saldanha Bay ports for the movement of cargo would be permitted.
"Furthermore, allowance will be made for South African-registered seafarers to embark and disembark ships with a mandatory quarantine for those returning.
"To this extent, the South African Maritime Safety Authority shall be directed to issue a marine notice to this effect."
Mbalula added the transport department's commitment to the preservation of human life was informed by the Constitution.
"Consultations we had with industry bodies, across various modes of transport, have given us confidence that the majority of the sector is ready to resume operations with strict adherence to health protocols.
"We have taken note of advisories from the World Health Organisation and Department of Health discouraging the use of sanitising booths due to health concerns. We will ensure that these are not utilised at our transport facilities."
He said the transport sector should be responsive to enable the mobility of both workers and pupils as Grade 7 and 12 pupils were expected to return to classrooms and more workers would be reporting for duty next week.
"The reopening of schools and some institutions of higher learning in June require of us to put measures in place to enable the safe movement of learners and students."
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