In a briefing to the media on Saturday, Transport Minister Fikile Mbalula advised on what the restrictions would be under alert level 3 of the lockdown, starting on 1 June.
He said that so-called "sanitation booths" would not be allowed for commuters after the World Health Organisation advised against these.
On Friday evening, Professor Salim Abdool Karim, the chairperson of the Ministerial Advisory Committee on Covid-19, said: "Human spraying is harmful with almost no benefit."
He said simply spraying hands properly with a sanitiser was the best way to prevent the spread of the virus.
His views put paid to the plans of the Gauteng department of roads and transport, which tried out sanitation tunnels at minibus taxi ranks.
Some people had even suggested that the tunnels could be used at schools when some pupils returned on Monday.
Abdool Karim was backed up by infection control specialist Professor Shaheen Mehtar, who said: "There is no need for a disinfection tunnel.
"And there is no need to spray any children with a chemical."
On Saturday, Mbalula said that with more industries resuming operations and learners returning to school, the transport sector needed to be responsive to enable the mobility of both workers and learners.
"In doing so, we must maintain a delicate balance between enabling mobility and arresting the spread of the virus. Our commitment to preservation of human life above all else, is informed by our constitution, which enjoins us in ensuring that the right to life is non-derogable and therefore supersedes all other rights.
"The consultations we have held 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."
He said they had taken note of advisories from the World Health Organisation and department of health discouraging the use of sanitising booths due to the health concerns.
"We will ensure that these are not utilised at our transport facilities.
"So tough luck to those who thought this is good business, they will have to think of other innovations."
You can watch the rest of the briefing below:
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