Its International Human Rights Clinic (IHRC) said successive governments including the current administration had not complied with international law, reacting too slowly and doing too little to reduce the harm from abandoned and active mines near the "City of Gold".
The report said the government gave only limited warnings of the risks, did not perform enough scientific studies on the health effects, and rarely engaged with residents.
The Department of Environmental Affairs could not immediately comment on the findings of the Harvard report.
Pollution of ground and surface water from acid mine drainage and contaminated dust and soil from mine dumps have exposed residents living around the mines and on the waste dumps to high concentrations of heavy metals and radiation "that can contribute to immediate and long-term medical problems ranging from asthma and skin rashes to cancer and organ damage," the report said.
It added: "The government's response to the crisis has been insufficient and unacceptably slow" and piecemeal, falling short of its duties under human rights law.
The South African Chamber of Mines, which groups several mining companies in Africa's most industrialized country, said it could not comment because it had not read the report yet.
"The Chamber was not approached to provide input by the authors prior to or post the publication of the document," said the Chamber of Mines.
South Africa's government said it had set aside an estimated 1.2 billion rand ($87 million) in 2011 to clean up acidic water threatening to spill out from abandoned gold mines under Johannesburg.
In May, South Africa gave the go-ahead for class action suits seeking damages from gold companies for up to half a million miners who contracted the fatal lung diseases silicosis and tuberculosis.
Some local environmentalists supported the IHRC report.
"There is often a systemic failure on their part to enforce the legislation," said CEO of the Federation for a Sustainable Environment, Mariette Liefferink, endorsing recommendations to minimize further risks and remedy current harm caused by contamination.
(Editing by James Macharia/Ruth Pitchford)