The Gift of the Givers humanitarian aid organisation says it knows nothing about a ransom of more than R50m that was allegedly paid for the release of Stephen McGown, Netwerk24 reported on Friday.
McGown was held hostage by al-Qaeda in Mali for six years. His release at the weekend was officially announced at a media briefing in Pretoria on Thursday.
International Relations and Co-operation Minister Maite Nkoane-Mashabane said at the news conference that no ransom had been paid.
However, the New York Times in its report on McGown's release, quoted a retired European intelligence official as saying that a ransom of €3.5m had been paid.
The source claimed that the Gift of the Givers had arranged the payment of the ransom though an agent in the French intelligence service.
Gift of the Givers founder Dr Imtiaz Sooliman said on Thursday evening that he didn't have a clue where the paper got its information.
"The French haven't been involved in negotiations for McGown's release for the past two years because we had warned them that al-Qaeda considered them to be its enemies and it would have jeopardised negotiations," said Sooliman.
"We helped facilitate the negotiations, arranged contact between the parties and left the negotiations to the government at the end of June."
Sooliman said talks between the governments of South Africa and Mali, as well as their intelligence services, had been essential.
The last phase of the negotiations would not have been possible without the support of the army and the use of private helicopters and planes.
"We couldn't be involved in any of these arrangements and therefore have no information about a ransom purportedly having been paid," said Sooliman.
'Only they know where they got the story'
He said he also found the New York Times allegation very strange, as the South African government had taken full credit for McGown's release, without mentioning the Gift of the Givers.
"Our negotiator hasn't been in Mali for the past four months, so only they know where they got the story that someone had met with a French agent."
McGown was taken hostage with Swede Johan Gustafsson and Sjaak Rijke of The Netherlands.
Gustafson was released in June, while France's special forces freed Rijke in April 2015.
McGown's mother died in May. Sooliman earlier said she had been ill for several years and that her condition had deteriorated over the past few months.