The government has spent at least 200 million rand (USD 20 million) to revamp Zuma's rural home -- including a swimming pool and an outdoor amphitheatre -- justifying it as necessary security for a head of state.
But a government watchdog in a report titled 'Opulence on a Grand Scale' has found that Zuma derived "substantial" benefit from the deal, South Africa's weekly Mail & Guardian reported.
Some of the so-called security upgrades were "improperly" weaved into the project at "enormous cost" to the taxpayer, it said.
South Africa's public protector investigates reported abuse of power by public officials, publishes the findings, and recommends prosecution where needed.
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Madonsela wants Zuma to explain himself to parliament and repay the extra non-security expenses, the paper said citing the report.
The improvements at Zuma's house were "acutely" better than those done at past presidents' properties, said the report.
She also said "genuine" security issues such as the two helipads, a clinic and housing for the police protection unit at the thatched-roof compound were "excessive". Above all, they could have been located in a nearby town to also benefit local residents, the report said.
The public protector's office declined to comment on the newspaper's story on Friday, but last week Madonsela said four ministers seen as Zuma's loyalists, had tried to vet her report by approaching the court to instruct her on what to "throw out and what to retain".
The exact cost of the upgrades remains unclear. Two weeks ago, a parliament panel put it at 206 million rand (USD 20.2 million). The Mail & Guardian reported the costs at 215 million rand.
Zuma's office did not respond to phone calls and an email seeking comment.