A new report by the South African Medical Research Council (SAMRC) has found more than 133,000 deaths from Covid-19 took place over the past year.
As of Wednesday, the official death toll was around 54,900 since the start of the coronavirus pandemic.
The new report looked at excess deaths in the country, which has been Africa’s worst-hit by the Covid-19 pandemic in terms of the number of fatalities and infections to date.
It found there had been 157,000 excess deaths in the past 12 months, with 85 per cent of them caused by coronavirus.
This equates to just over 133,000 deaths from the virus.
Excess death figures - which some epidemiologists say are the best way to measure the true toll from Covid-19 given varying official counting methods - surpass many official death tolls for coronavirus.
It typically looks at the difference between the observed numbers of deaths in specific time periods and expected numbers of deaths in the same time periods.
The SAMRC report said the excess death rate per 100,000 population for South Africa was 258 over the past 12 months.
This places the country - on an age-standardised basis - in the top five countries for which excess deaths are measured.
The health ministry declined to comment immediately on the report.
Last year, South Africa imposed tough lockdown measures to curb the spread of Covid-19, including border closures and even bans on the sale of alcohol and cigarettes.
Most restrictions have now been lifted but a recent rise in infections has prompted fears of a third wave of the pandemic.
Towards the end of last year, a new coronavirus variant was detected in South Africa - which drove its second wave - and spread to other nations around the world.
This variant quickly went on to dominate infections across the country, accounting for around 90 per cent of cases nationally earlier this year.
It was announced last week several cases of a new coronavirus variant first detected in India - currently in the throes of a second wave of Covid-19 - had been found in South Africa for the first time.
There have been 1.6 million cases of coronavirus reported in South Africa since the start of the pandemic to date.
Additional reporting by Reuters