The SAFA leadership, which includes president Kirsten Nematandani, vice-presidents Mandla Mazibuko, Dr Danny Jordaan, Dr Irvin Khoza, Chief Mwelo Nonkonyana, Alpha Mchunu and CEO Dr Robin Petersen - released a statement condemning the recent claims in the media.
"We are united in our condemnation of these reports," said Nematandani in the statement.
"They seek to create divisions where there are none, and to falsely create an impression that SAFA LOC (Local Organising Committee) board members will profit from the hosting of AFCON 2013.
"We have undertaken to investigate both the purported facts of these reports, as well as the source of the leaks that have led to these. Strong action will be taken against anyone who is found to have been a part of these malicious leaks and allegations."
The probe will also scrutinise reports that indicated there are plans afoot to depose Nematandani as president.