Professor Salim Abdool Karim, who served as the government's chief adviser during the initial response to the pandemic, also said it was too early to say whether omicron led to more severe clinical symptoms than previous variants.
However, he said it did appear more contagious and more likely to infect people with immunity from vaccination or prior infection, and he was expecting it to drive new daily infections in the country above 10,000 before the end of the week, from 2,858 on Sunday.
"Based on what we know and how the other variants of concern have reacted to vaccine immunity, we can expect that we will still see high effectiveness for hospitalisation and severe disease, and that protection of the vaccines is likely to remain strong," Abdool Karim told a news conference.
Preventing severe disease is mainly a function of T-cell immunity, different from the antibody immunity that often blocks infections, "so even if there's some escape from antibodies it's very hard to escape T-cell immunity", he said.
The discovery of the variant in southern Africa has caused a strong global reaction, with countries limiting travel from the region and imposing other restrictions for fear it could spread quickly even in vaccinated populations.
The World Health Organisation said on Monday that the variant posed a very high global risk of infection surges, though further research was needed to assess its potential to evade protection against immunity induced by vaccines and previous infections.
South African doctors who have treated COVID-19 patients say Omicron so far appears to be producing mild symptoms, including a dry cough, fever and night sweats.
Abdool Karim, a professor at South Africa's University of KwaZulu-Natal and Columbia University in the United States, said no "red flags" had been raised so far.
However, it was too early to draw firm conclusions, because doctors can only comment on patients who they treat. "There's not enough data yet," he said.
South Africa's government is doing everything possible to prepare its health facilities to cope with the variant and is asking countries that imposed travel restrictions on southern Africa to reverse them, Health Minister Joe Phaahla told the same news conference.
Public health officials said Gauteng province, where cases have surged since the variant's discovery, had so far not seen an increase in COVID-19 deaths. It was not yet possible to say whether Omicron has caused any fatalities, they added.