The Aids policies of the former South African president Thabo Mbeki's government were directly responsible for the avoidable deaths of more than a third of a million people in the country, according to research by Harvard university.

South Africa has one of the severest HIV/Aids epidemics in the world. About 5.5 million people, or 18.8% of the adult population, have HIV, according to the UN. In 2005, there were about 900 deaths a day. But from the late 1990s Mbeki turned his back on the scientific consensus that Aids was caused by a viral infection that could be fought – though not cured – by sophisticated and expensive medical drugs. He came under the influence of a group of maverick scientists known as Aids denialists, most prominent among whom was Peter Duesberg from Berkeley, California. In 2000, Mbeki called together a round table of experts, including Duesberg and his supporters, but also their opponents, to discuss the cause of Aids. Later that year, at the International Aids conference in Durban, he publicly rejected the accepted scientific wisdom. Aids, he said, was brought about by the collapse of the immune system – but not because of a virus.

The cause, he said, was poverty, bad nourishment and general ill-health. The solution was not expensive western medicine, but the alleviation of poverty in Africa.

In a new paper (PDF), Harvard researchers have quantified the death toll of Mbeki's stance, which caused him to reject offers of free drugs and grants and led to foot-dragging on the part of his government over bringing in a treatment programme, even after Mbeki – under intense international criticism – had taken a vow of silence on the issue.

"We contend that the South African government acted as a major obstacle in the provision of medication to patients with Aids," write Pride Chigwedere and colleagues from the Harvard school of public health in Boston in the Journal of Acquired Immune Deficiency Syndrome.

They have made their calculations by comparing the scale-up of treatment programmes in neighbouring Botswana and Namibia with the limited availability of drugs in South Africa between 2000 and 2005. Expensive antiretrovirals (ARVs) came down in price dramatically as a result of activists' campaigning and public pressure. In July 2000, the pharmaceutical company Boehringer Ingelheim offered to donate its drug nevirapine, which could prevent the transmission of HIV from mother to child during labour. But South Africa restricted the availability of nevirapine to two pilot sites per province until December 2002. Under international pressure, South Africa did eventually launch a national programme for the prevention of mother-to-child transmission in August 2003 and a national adult treatment programme in 2004. But by 2005, the paper's authors estimate, there was still only 23% drug coverage and less than 30% prevention of mother-to-child transmission.

By comparison, Botswana achieved 85% treatment coverage and Namibia 71% by 2005, and both had 70% coverage with mother-to-child transmission programmes.

The authors estimate that more than 330,000 people died unnecessarily in South Africa over the period and that 35,000 HIV-infected babies were born who could have been protected from the virus and would probably have a limited life. Their calculations will withstand scrutiny, they say. "The analysis is robust," said Chigwedere. "We used a transparent and accessible calculation, publicly available data, and, where we made assumptions, we explained their basis.

"We purposely chose very conservative assumptions and performed sensitivity analyses to test whether the results would qualitatively change if a different assumption were used."

The authors conclude: "Access to appropriate public health practice is often determined by a small number of political leaders. In the case of South Africa, many lives were lost because of a failure to accept the use of available ARVs to prevent and treat HIV/Aids in a timely manner." Following Mbeki's ousting from the leadership of the African National Congress in September, South Africa is now urgently pursuing new policies to get treatment to as many people as possible under a new health minister, Barbara Hogan.