Nathi Nhleko said that the upgrades, including a pool costing almost 4 million rand ($328,000) were in fact security features.
In 2014, an independent inquiry found Jacob Zuma had “unduly benefited” from the upgrades.
Jacob Zuma has been heavily criticized over the issue.
In February, the Nkandla controversy prompted chaotic scenes in parliament as leftist lawmakers scuffled with security.
They had been interrupting a key annual speech by Jacob Zuma and demanding answers over the row.
In 2014, a report by South Africa’s anti-corruption watchdog found Jacob Zuma had “unduly benefitted” from the renovations and recommended he pay back some of the money.
However, Jacob Zuma has maintained he would only pay money back if ordered to do so by Nathi Nhleko.
At a news conference Nathi Nhleko justified his decision not to make Jacob Zuma pay back any of the money by saying the upgrades were security features.
For example, Nathi Nhleko explained the pool was in fact intended for use in fighting fires, and he even had a video of four policemen demonstrating how this security feature worked.
A chicken run, a cow enclosure, an amphitheatre and visitors centre were also all classed as security features by Nathi Nhleko.
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