This comes after the country`s highest court ruled earlier this year that Mr Zuma repay some of the $23m of public funds spent on his house in 2009.
The upgrades included an amphitheatre, pool, chicken run and cattle enclosure.
Mr Zuma must now repay the money - about 3% of the total spent - within 45 days.
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An anti-corruption body, known as the public protector, ruled in 2014 that Mr Zuma had "unduly benefited" from the non-security renovations to his rural home in Nkandla in South Africa`s KwaZulu-Natal province.
In March, the Constitutional Court then ruled that he had violated the constitution when he failed to repay some of the money.
It gave the treasury two months to come up with a figure for Mr Zuma to repay.
The treasury says it hired two independent quantity surveyors to conduct separate investigations to come up with the figure.
The main opposition Democratic Alliance (DA), one of the parties which brought the case, welcomed the treasury`s report but said it had hoped the figure would be higher.
"This sends out a clear message to those involved in corruption, especially those in the ANC, that you will be held accountable for your actions, even if you are the president," the AFP news agency quotes DA spokesman Mabine Seabe as saying.
South Africa`s President Zuma `must repay $500,000 in public funds`
28 June 2016
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South Africa`s treasury has recommended President Jacob Zuma pay back $509,000 (£385,000) to the government for upgrades made to his private home.
