Fikile Mbalula, however, said he couldn't say what Warner did with the money, which South Africa claims was "above board" and meant for soccer development in the Caribbean region.
What happened to the cash is "another story for investigators ... We don't know," Mbalula said. "We can't account for that."
Mbalula repeated the South African government's denials that the country paid bribes to win the right to host the 2010 tournament, as alleged in indictments from the US Department of Justice.
"We therefore wish to categorically deny that our country and government have bribed anyone to win the rights for the 2010 FIFA World Cup," Mbalula said today at the headquarters of the South African Football Association.
The Justice Department believes that USD 10 million was sent by South Africa, through FIFA, to Warner in three wire transfers in 2008 as payback for him and two other then-FIFA executive committee members for backing South Africa in the 2004 vote.
South Africa won the World Cup by four votes over Morocco, making the ballots of Warner and his two "co-conspirators" decisive.
Mbalula also insisted that the South African government had not contradicted itself after the emergence of a leaked letter from then-South African Football Association president Molefi Oliphant in 2008 asking FIFA secretary general Jerome Valcke to send the USD 10 million to Warner from South Africa's World Cup funds.
Oliphant twice specified in the letter that the implicated Warner be in control of the money.
"The letter leaked to the media, we don't know why it was leaked in the first place because that correspondence was above board," Mbalula said, denying it suggested a bribe was paid. "Criminals can explain a bribe very well. I don't know how bribes work.
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