Although FIFA had already dismissed any allegations over the improper use of the R450m legacy fund it left South Africa from the 2010 World Cup, the front-page story in South Africa's Sunday Times was another indication of the crisis facing the national federation, which will soon be investigated by the government after a dramatic three-year decline since the landmark first World Cup in Africa.
The ongoing allegations of major financial mismanagement and corruption within SAFA over possible match-fixing just before the World Cup have led to clear concerns from the South African government and national Olympic committee over the running of football.
SAFA's troubles have also created friction between South Africa and former partner and world body FIFA over the scope of the upcoming government-led investigation, which the football parties want to be limited to just investigating match-fixing. The sports ministry and South African Sports Confederation and Olympic committee feel there are more problems to be looked into, and the country's independent judicial inquiry into football has gone right to the top, with President Jacob Zuma set to decide on the parameters of the investigation.
In biting criticism of SAFA, the sports ministry and Olympic committee referred this month to the "crisis and pending implosion" of the federation in charge of South Africa's most popular sport when it asked Zuma to decide on how extensive the investigation should be. Zuma's office said the president would take into account various protocols, including FIFA's rules against governments interfering in independent football bodies, but the government's obvious frustration with SAFA may lead it to a fuller probe.
That would push South Africa toward an international football ban by FIFA.
Meanwhile, in its report, The Sunday Times raised concerns over the use of around $12m (R109m) of World Cup money, which it said was separate to the main legacy fund and moved to SAFA's accounts over the past two years. The newspaper also said SAFA had just $318 000 (R2.9m) in the bank at the end of the financial year in 2012. The newspaper said it had seen figures from an audit of SAFA's accounts for the year up to June 2012, which showed the federation had made a loss of R54.5m rand and "burned cash" when it was struggling with diminished sponsorship.
The World Cup's legacy money is meant to be used for developing grassroots football.
Although there is little clarity yet on SAFA's finances, and it is uncertain if the upcoming investigation will uncover any of the alleged links between match-fixing syndicates and SAFA officials, there is no doubt the association's deep problems are undoing some of the good work of the widely-praised World Cup and could end up damaging the country's relationship to FIFA.
In a statement to The Associated Press this month, FIFA stressed that no money from the main $50m (R455.5m) legacy fund could have been used improperly because the trust is controlled jointly by SAFA, FIFA, the South African government and business sector, and is administered by an independent auditing firm.
But at the same time, FIFA has compelling evidence that points to match-fixing in some of the South African national team's warm-up games ahead of the World Cup, where SAFA officials may have allowed match-fixers to appoint corrupt referees to officiate games.
Alone, "this long-standing open case is harming South African football," FIFA secretary general Jerome Valcke said.