On Monday Super Falcons chairman Bob Maredi told KickOff.com he suspected foul play in a Gauteng Sasol League title decider with Mamelodi Sundowns Ladies last Saturday.
Maredi questioned many of the decisions from the officials in the unruly season-finale, which had to be halted when an outraged Falcons player reportedly kicked the referee in the chest at Chloorkop.
SAFA on Thursday announced they would investigate the issue.
Khumalo suspects the incident is not an isolated one.
"It's not only in Joburg. According to reports I've seen in Limpopo and stuff, maybe I can say our football is rotten to its core,'' Khumalo told this website.
"I'd say there are lot of things. I always say, sometimes we don't take things serious until something major like this happens. When we talk about the development of football, when you talk about how to develop things, we focus on one aspect and there are major issues that needs to be strengthened to ensure that there's progress in our football.
"How do you develop a player to play good and then for the officiating not to be good? It still doesn't allow the players to grow. How do you develop players if your administration is poor?
"To tell you about the game of Sundowns against Super Falcons, I was there. I saw the game and of course I was talking to some players from both sides, so it's pretty bad.
"But what I can also say, discussing it or debating about it with some other people, the 23 players that played, I said to them 'We shouldn't be putting you in the middle of this', because the players become victims of this thing. For the players their job is to play and both set of players went to the field to play football and try to help their teams win."
SAFA spokesman Dominic Chimhavi warned of the dangers of jumping to conclusions without proof.
"That is unfounded allegations, you can't make such an allegation without proof. I mean, a referee sometimes can have a bad day, it's a global phenomenon and sometimes officials can have a bad day," Chimhavi told this website prior to SAFA announcing they would probe the matter.
"You can't equate a bad day to match-fixing, that is serious allegations which is very unfounded and it is unfortunate that someone makes such allegations... It is not true and there's no shred of evidence on such allegation.
"Arsenal manager Arsene Wenger was on television, to the global audience, to say the referee for their game against Manchester City was atrocious and he said he never seen such poor refereeing. If it can happen in England, it can happen in SA. I'm not saying I'm condoning it, but we don't condone that.
"We are saying if an official had a bad day don't equate that to match-fixing... it's wrong and damaging allegations and unfounded. It's not true."
Among the complaints surrounding the match between Sundowns Ladies and Super Falcons was that there was only a referee and one assistant referee. Asked about this, Chimhavi said: "The rule says, by any chance a linesman doesn't pitch up to the match, the match should go ahead.
"Also what the referee did on the day is that he went to both teams to say, 'Look here, one of the lineman is not here, they failed to pitch up,' and both teams agreed that the match should go ahead, which is the norm to say, if a lineman doesn't pitch up normally the match should go ahead.
"Only after consulting with both teams, which is what the referee did on Saturday, both teams agreed that the game should go ahead."
KickOff.com also contacted Sasol League PR manager Njabulo Mbatha, who said any complaints they receive are directed SAFA's way.
"Anything we hear we raise to SAFA and SAFA then can comment, not us as the sponsorship."