Speaking at a media briefing in Johannesburg on Tuesday, Mbalula said he was seeking an urgent meeting with SAFA to discuss this thorny issue.
Asked if the allegations by FIFA into match-fixing allegations will also be on the agenda, Mbalula said: "It's one of them but there are a variety of issues to be discussed.
"We will also look at the dismal performance of Bafana Bafana in the 2012 Africa Cup of Nations qualifiers, which saw them fail to go to the tournament for the second successive time after missing out in 2010 in Angola. We are making this call (to SAFA) amid cries of the nation in recent performances of our national teams, especially Bafana Bafana."
The minister said he will meet SAFA with the South African Sports Confederation and Olympic Committee, whom he met on Tuesday to discuss 2012 London Olympics preparations.
"We will also not tolerate the infighting among the leadership of SAFA that at the end of the day compromises the performance of our teams and the moral fibre of our football, said Mbalula."