Many people who died from HIV/Aids were recorded as having died of related illnesses such as pneumonia and tuberculosis, the council said. The stigma still attached to the disease had helped keep figures artificially low.
In research published in the journal Aids, the article's authors estimate that more than 112,000 people died of HIV-related illnesses in 2000-01, almost three times the number given by South Africa's department of home affairs.
The article adds that about 74 per cent of children under five who died in the same year died of HIV/Aids-related illnesses, rather than the 25 per cent that government figures suggest.
Dr Debbie Bradshaw, a co-author of the report, said: "A large proportion of deaths due to HIV infection are misclassified [on death certificates] as the opportunistic infections that are the immediate cause of death."
She added that many doctors were reluctant to certify deaths as due to HIV because the family may then struggle to claim life insurance or funeral policies. The bereaved also did not want to have to deal with the social stigma of the disease.
The findings add fuel to a continuing battle between medical workers and government officials, who are often reluctant to reveal the true extent to which HIV/Aids has hit the country.
In 2002, a survey by the government agency Statistics South Africa showed that only 8.7 per cent of deaths in the country were caused by HIV/Aids, but medical researchers and Aids charities insisted at the time that it had downplayed the scale of the pandemic.
The medical research council warned that the agency's latest survey, to be released this week, will again underestimate the number of Aids deaths in the country. Statistics South Africa was to have published its report on 12 January, but many believe it has been delayed because of political considerations.
President Thabo Mbeki has come under fire in the past for downplaying the problem of Aids; for years he questioned the link between HIV and Aids and delayed implementing Aids-prevention programmes. Much to the fury of health workers, the government had in the past warned that Aids drugs were unsafe, and had refused to provide antiretrovirals to prevent mother-to-child HIV transmission.
President Mbeki has now softened his stance on Aids, but in the meantime South Africa is believed to have developed one of the highest rates of HIV/Aids in the world. Detractors say President Mbeki's attitude towards Aids is far less realistic than that of his predecessor, Nelson Mandela, who announced three weeks ago that his last surviving son had died of the disease.
The lobby group Treatment Action Campaign said the research council study showed that South Africa had fallen behind the rest of the world. "Given the political climate and the resultant disincentives for reporting HIV/Aids in the South African setting, it is probably not surprising that the level of reporting of HIV or Aids as a cause of death is low," the group said. "This is in stark contrast to Brazil where a policy of universal access to free treatment was implemented early in the epidemic and the level of reporting on HIV on death certificates is over 85 per cent."