FIFA sent a letter to the South African sports ministry and football association on Thursday warning against government interference in the sport.
FIFA said secretary general Jerome Valcke's letter to both sports minister Fikile Mbalula and South African Football Association president Kirsten Nematandani reminded them to respect an agreement that a government-appointed independent commission was restricted to just investigating allegations of match-fixing ahead of the 2010 World Cup, and no other issues inside the national football federation.
FIFA's warning came after a statement critical of SAFA was released by the sports ministry and the government-aligned Olympic committee this week, hinting that the government was losing patience with a football federation that has been beset by problems since the country's hosting of the World Cup three years ago.
That statement raised the possibility of an independent investigation into allegations of financial mismanagement, as well as match-fixing.
FIFA confirmed that some of the contents of Valcke's letter referred to government interference, while SAFA published a part of it in a statement.
The federation is believed to be unhappy at the South African government's apparent intention to launch a wider investigation into its affairs.
On Tuesday, the sports ministry and South African Sports Confederation and Olympic Committee (SASCOC) said the government might look into other problems, including allegations SAFA was $10 million in debt. The government also noted allegations regarding the distribution of money given to South Africa by FIFA after the World Cup.
The sports ministry said there had been reports of a 'crisis' within SAFA as far back as November 2010.
"The ministry also painstakingly observed a barrage of negative publicity and public outcry precipitated by allegations of leadership squabbles, financial mismanagement and maladministration,'' the sports ministry and SASCOC said in their joint statement.
South Africa's government is still working on the makeup of a judicial commission to look into the allegations that South African national team games were fixed in the weeks before the World Cup. But the sports ministry also warned that it was within its rights to also look at other possible problems. That would break an agreement with FIFA, the world football body.
The sports ministry said South Africa's government was 'empowered... to intervene in reported instances of maladministration and mismanagement. We indicated that in terms of our laws, match-fixing/match manipulation and financial mismanagement are considered as acts of criminality."
FIFA has strict rules against government interference in what it views as football matters.
"In regards to SAFA's internal matters, these must be handled by SAFA internally through its bodies or any other footballing bodies and not by government,'' FIFA said in a statement to The Associated Press later on Thursday.