FIFA said the three payments totalling $10 million mentioned in a U.S. federal indictment, which are at the heart of a Department of Justice probe, were approved in 2007 by Julio Grondona, the former chairman of the finance committee who died last year.
The FIFA statement follows a New York Times report that American law enforcement officials believe secretary general Jerome Valcke transferred the money in 2008 to accounts controlled by Jack Warner, the former CONCACAF president and FIFA vice-president who faces corruption charges in the U.S. The report cited unidentified law enforcement officials.
American investigators say Warner's long-time FIFA colleague, Chuck Blazer, believed the money was paid as bribes in exchange for their votes to give the 2010 World Cup to South Africa.
While a FIFA statement did not deny Valcke knew of the payments in 2008, it said neither he "nor any other member of FIFA's senior management were involved in the initiation, approval and implementation" of the project.
Valcke's awareness of the $10 million appeared to be confirmed by a letter to him dated March 4, 2008, from then-South African Football Association president Molefi Oliphant. The South African Broadcasting Corporation published the letter.
In it, Oliphant asks Valcke for FIFA to withhold $10 million from South Africa's World Cup organizing budget and advance it to a fund called "Diaspora Legacy Program."
Oliphant twice notes that Warner, then Grondona's deputy on the finance panel, should control the money.
When contacted by The Associated Press last week, Oliphant declined to comment on the bribery allegations made by the DOJ. He did not answer a call seeking comment on Tuesday.
The World Cup bidding angle is a direct route into FIFA for the Department of Justice, which laid out a racketeering case mostly involving marketing rights for tournaments in North and South America over two decades.
That led to seven officials being arrested last week — including two FIFA vice-presidents, one newly elected FIFA executive committee member and a FIFA staffer. They were among 14 people named in a racketeering indictment accusing soccer officials of accepting more than $150 million in bribes. Four more people, including Blazer and two of Warner's sons, had their guilty pleas unsealed.
The South African allegation threatens to tarnish a 2010 World Cup which FIFA President Sepp Blatter has claimed as a defining achievement of his 17-year reign.
FIFA described the payment on Tuesday as part of the South African government's "project to support the African diaspora in Caribbean countries as part of the World Cup legacy."
It said the payments were authorized by Grondona "in accordance with the organization regulations of FIFA."
Grondona served as a member of FIFA's executive committee for 26 years. The Argentine was the senior FIFA vice-president — No. 2 to Blatter at the boardroom table — when he died last year at the age of 82.
The 79-year-old Blatter, who won re-election Friday for a fifth term despite the scandal, denied being the unidentified high-ranking official named in the indictment as having "caused" the payment.
"Definitely that is not me," Blatter said Saturday at a news conference.
Prince Ali, the Jordanian who lost to Blatter in last week's presidential election, told CNN that Blatter should resign because of the widening scandal.
"If I was in Sepp Blatter's position, I would have immediately resigned and probably more so ages ago because at the end of the day, this happened under his watch," the prince said.
In South Africa, former President Thabo Mbeki has denied his government paid bribes to secure the World Cup. Danny Jordaan, the bid chief for the 2010 tournament, told a South African newspaper that the money was sent to Warner's regional confederation to help with soccer development in the Caribbean.
FIFA announced Monday that Valcke had cancelled his planned trip to attend the opening of the Women's World Cup in Canada on Saturday "due to the current situation."
The fallout continued this week for the South American regional body, known as CONMEBOL, and the North American region, known as CONCACAF.
The scandal threatens the marquee Centennial Copa America tournament, due to be played in the United States next June. The indictment detailed a $110 million bribe scheme for the event and named officials from three marketing firms which own the broadcasting rights.
Nicolas Leoz, an 86-year-old former CONMEBOL president and long-time FIFA executive committee member, was ordered under house arrest in Paraguay. The foreign ministry confirmed a request from the United States Embassy for Leoz's arrest and to seek his extradition.
The seven men detained in Zurich are fighting extradition.
In a separate case in Brazil, long-time FIFA executive Ricardo Teixeira is being accused of corruption crimes related to $147 million in bank transfers as he led the preparations for the 2014 World Cup.
Teixeira and Leoz both resigned from FIFA while implicated in a World Cup kickbacks scandal which was resolved in 2013.
AP Sports Writer Gerald Imray in Cape Town, South Africa, contributed to this report.