South Africa has denied paying a $10m bribe to secure the 2010 World Cup, in the wake of a US inquiry into corruption at world football body Fifa.
Sports Minister Fikile Mbalula said the money in question was above board and intended to support football in the African diaspora in the Caribbean.
The Fifa scandal erupted last week when US prosecutors indicted 14 people.
On Tuesday, president Sepp Blatter said he was to step down, just days after he had been re-elected.
Of the 14 indicted by the US on charges of racketeering and money laundering, seven were senior Fifa officials, including two vice-presidents. The seven were arrested in Switzerland as they awaited the Fifa congress and are currently awaiting extradition to the US.
The US justice department alleges the 14 accepted bribes and kickbacks estimated at more than $150m (£97m) over a 24-year period.
US officials quoted in the New York Times also said on Tuesday that Mr Blatter, 79, was under investigation as part of the inquiry. They said they hoped some of the Fifa figures charged would help to build a case against him.
US officials allege South Africa paid a $10m bribe in exchange for support for its 2010 World Cup bid from former Fifa vice-president Jack Warner and several other members of the North, Central American and Caribbean Association Football (Concacaf).
But in a press conference on Wednesday, Mr Mbalula said South Africa “categorically denied” the allegation, adding that the money went towards an approved programme.
How Fifa makes and spends its money
“We refuse to be caught up in a battle of the United States authorities and Fifa,” he said, adding that South Africa would cooperate with the US investigation.
Separately, Interpol issued a wanted persons alert for two former Fifa officials, including Jack Warner, as well as four corporate executives. All six were on the list of US indictments last week.
Announcing his resignation on Tuesday, Sepp Blatter said it appeared the mandate he had been given in last Friday’s Fifa vote “does not seem to be supported by everyone in the world”.
He said he would continue in his post until an extraordinary congress was called to elect a new president.
No dates have been set, but it is expected to take place between December 2015 and March 2016.
Analysis: Richard Conway, BBC Sport, Zurich
Sepp Blatter’s key advisers cut dejected figures last night as their boss announced he was stepping aside.
The air of despondency in Zurich contrasts sharply with that in the rest of Europe. English Football Association chairman Greg Dyke and others who have pushed for reform rejoiced at the news that the man who has controlled Fifa with an iron grip since 1998 was finally going.
The question now turns to who will replace Sepp Blatter. What sort of Fifa will the winner inherit if the promised radical reforms take place? What next for the World Cup hosts Russia and Qatar?
Unless the electoral process changes dramatically Asian and African countries will once again be the power brokers.
Given anti-European sentiments amongst many nations in those continents the winner will need to be acceptable to all sides.
With Prince Ali of Jordan backed by Uefa, could he now return and claim the Fifa crown he was denied by Sepp Blatter last Friday?
Why did Sepp Blatter go now?
Resignation speech in full
Reaction from footballing world
How would Fifa officials be extradited?
Mr Blatter was back in his office at Fifa headquarters in Zurich on Wednesday, the BBC understands.
His daughter, Corinne Blatter-Andenmatten, is quoted by Swiss Daily Blick (in German) as saying her father’s decision “has nothing, absolutely nothing, to do with the allegations going around”.
A separate criminal investigation by Swiss authorities into how the 2018 and 2022 World Cups were allocated is also under way.
Australian football chief Frank Lowy said in an open letter on Wednesday that the race to win the 2022 bid, which was awarded to Qatar, was “not clean” and that he had shared what he knew with the authorities.