South Africa will vaccinate 40-million people or two-thirds of its population against Covid-19 in order to achieve herd immunity, its health minister said on Thursday, as a mutant variant drove daily new cases above 21 000 for the first time.

A more contagious coronavirus mutant, first found on South Africa's east coast late last year, is driving a second wave of infections across Africa's most industrialised nation, pushing its total to 1.15-million, a third of all the continent's cases.

This week, deaths in South Africa surpassed 30 000, and Health Minister Zweli Mkhize said both private and public hospitals were struggling to manage to a growing influx of patients.

"Deaths and admissions are already higher than what we have ever experienced before," he said in virtual presentation to parliament.

Mkhize proposed vaccinating the 40-million people over a year -- without saying when they would start -- a goal he admitted was "a huge task", given the country's capacity in terms of staff and facilities.

"We need 67-70% of the population to be immunised to break the cycle of transmission ... (and achieve) herd immunity," he said.

Mkhize reiterated that South Africa aimed get its first vaccines in February and laid out a model for how procurement might work.

Some 70% would come from AstraZeneca, whose shots were the cheapest at R54 per dose, while Johnson & Johnson would get a 20% allocation, and Pfizer and Moderna 5% each. South Africa has yet to sign a deal with any of them. It is participating in the COVAX initiative co-led by the World Health Organization but that covers just 10% of its populace.

"The department has approached a number of vaccine manufacturers and discussions are at a sensitive stage," Mkhize said, adding that he believed talks would soon conclude.

The cost would come to R20.6-billion if they managed to achieve the targeted 67% coverage of the population, the model showed.

Priority would go to 1.25-million health workers, then a second phase would target other essential workers, people over 60 and people with co-morbidities, 8-million in total, then the rest would be vaccinated in a third phase, Mkhize said.

He acknowledged criticism from doctors that the government had moved to slowly on vaccine procurement, but added: "the government is on course ... vaccines will be made available."