The flamboyant Fulham owner vented his fury at the players at the club's training ground on Tuesday - their first day back following the humiliating defeat against Hughes' former employers.
Al Fayed has been no stranger to controversy since he bought the club in 1997.
He slammed former manager Roy Hodgson for joining Liverpool after guiding the team through arguably its most successful period in history and once said FIFA was run by "idiots".
But the Egyptian, who is a regular at Fulham games, was not meddling in first-team affairs according to Hughes, who hopes the ticking off will inspire his team to a much-needed victory against Birmingham.
"Yes, he (Al Fayed) came down to the training ground," Hughes confirmed.
"He is obviously the chairman and takes a real active interest in the club.
"He's at all the home games and chats with the guys so it was good to see him.
"It was good that the players heard his views of the performance at the weekend.
"We had obviously already discussed what we felt about the game as a group of players and management so his input was noted and obviously we want to build on what we feel we have achieved this season in terms of performance level.
"We hope it helps us win the match."
Hughes denied that CFR Cluj striker Lacina Traore is on his wish list and hinted that acquiring the likes of Shay Given, Roque Santa Cruz and Shaun Wright-Phillips, who have all been linked with the club in media reports on Friday morning, would be beyond his means.
"We get linked with a lot of players here," the former Manchester United striker said.
"There were a number in the press today. More often that not they are wide of the mark and that's what I would suggest is the case with some of the names that have been mentioned."
Fulham's preparations for the match at Craven Cottage have been dealt a blow by the news that Andy Johnson has joined fellow strikers Bobby Zamora (leg) and Mousa Dembele (ankle) on the sidelines.
The 29-year-old, who has just returned from a nine-month layoff, injured his hamstring in training but Hughes played down fears that the hitman is set for another lengthy spell on the sidelines.
"Andy has a bit of irritation at the bottom of his hamstring," Hughes explained.
"We have to be careful with him obviously because he's had two back to back games after a long time out so we don't want to compromise him so we're erring on the side of safety."
Meanwhile, Alex McLeish admits there is still room for improvement at Birmingham despite celebrating three successful years in charge this weekend.
McLeish steered City to promotion back to the Barclays Premier League in his first full season at St Andrew's after replacing Steve Bruce as manager in November 2007.
Then Blues experienced their best ever top flight finish in being placed ninth last season after being the bookmakers favourites to make a quickfire return to the Coca Cola Championship.
Birmingham made a difficult start to the current campaign but four points from their last two matches with high-riding Manchester City and Chelsea have moved them away from the bottom three.
McLeish told Press Association Sport: "You are never satisfied and I don't think that is a bad thing.
"I think it is good when you keep testing yourself, keep pushing yourself, keep pushing the players and asking `can we do better' because you don't want to stand still.
"You are never happy. You always feel `we could be doing a little bit better' given some of the points we have lost this season and we should actually be better off."
McLeish has no fresh injury concerns as City strive for their first away win of the campaign.
Midfielder Craig Gardner's ankle problem is improving although he is not ready to return at Craven Cottage.
Number two keeper Maik Taylor is also making good progress with his shoulder problem and is likely to be available for the Carling Cup quarter-final with Aston Villa next Wednesday.
Source: DSG
