Mokoena, who is still a member of the National Executive Committee (NEC), has indeed resigned but will carry on his duties at the association.
He was appointed SAFA's acting CEO in November last year following the departure of Russell Paul.
Contacted for comment, Mokoena referred all questions to head of communications Dominic Chimhavi.
"Yes it's true [I'm no longer CEO]. The right person to talk to about this is Dominic, he is the spokesperson of this thing. Yes, I'm still with SAFA," Mokoena tells snl24.com/kickoff.
SAFA took issue with a recent report in a local publication that claimed Mokoena quit his post because the association is poised for retrenchments and a government bailout.
According to Chimhavi, Mokoena only left the position because his four-month contract had come to an end.
"If you go to the SAFA website you will see that when we appointed him he said he doesn't want to take it on a long-term basis because he is a businessman," Chimhavi explains.
"So that rubbish that was written... it baffles me because he never resigned, his contract came to an end and that was the agreement. Now we just stuck to the agreement.
"When you go to the SAFA website and punch 'Mokoena appointed' it's written in black and white that he would take it on a four-month basis, full stop."
It remains a mystery though why SAFA allowed Mokoena to step down without first finding his replacement.
"We are busy in the process of looking, we'll see," Chimhavi concludes.