South Africa on Thursday ended mask-wearing for school children despite a surge of infections driven by two new Omicron sub-variants of coronavirus.

Regulations requiring all students to mask up while in class expired at midnight and were not renewed, the health ministry said.

However, adults are still required to wear a mask in public indoor spaces, and limits on numbers attending large events remain.

South Africa has officially recorded more than 3.8 million cases and 100,407 deaths -- the highest toll across Africa -- and less than 45 percent of the adult population has been fully vaccinated.

"The only way we can protect ourselves and our loved ones against this pandemic and the current rising number of positive cases is through vaccination and adhering to preventative measures at all times," the health ministry said in a statement.

After a relative lull last month, numbers of new infections have been climbing, and on Wednesday, more than 6,100 new cases were detected.

Inbound travellers are still required to be fully vaccinated or show proof of a negative PCR test.

Indoor gatherings are limited to 1,000 people or half of the venue's capacity, while outdoor events are capped at 2,000 people. Attendees are required to be vaccinated or provide negative Covid-19 test.

World Health Organization chief Tedros Adhanom Ghebreyesus on Wednesday said that two Omicron sub-variants, BA.4 and BA.5, were behind the surge in cases in South Africa.

Tedros said it was "too soon to know whether these new sub-variants can cause more severe disease than other Omicron sub-variants."