South Africa’s sports minister says the decision to donate $10m (£6.5m) to Fifa to develop Caribbean football was made by former President Thabo Mbeki.
The payment, which South Africa denies was a bribe to secure the 2010 World Cup, is central to the Fifa scandal.
The claim comes after a letter emerged that appears to show officials seeking an indirect route for the transfer.
South Africa’s government said the letter did not contradict its statement that this was a legitimate payment.
It says the cash was to fund the development of football for the African diaspora in the Caribbean and that the reporting of the letter in South Africa’s Mail & Guardian was “regurgitation and sensation”.
The letter was written by then South Africa FA head Danny Jordaan three weeks before the first amount was paid in 2007.
US prosecutors say the money, which is a key plank in the wide-ranging criminal inquiry that has engulfed world football’s governing body, was a bribe to Fifa officials.
Seven top Fifa officials, including two vice-presidents, were arrested last week in Switzerland as they awaited Fifa’s congress.
They were among 14 new indictments in the US investigation, which alleges they accepted bribes and kickbacks estimated at more than $150m over a 24-year period.
Four other people were charged earlier. One of them, ex-Fifa official Chuck Blazer, has pleaded guilty in the US to taking bribes related to South Africa’s bid.