The Egyptian businessman has demanded a review of both refereeing practices and the decision-making process. He has written to both the FA and Premier League seeking action on behalf of all clubs.
Al Fayed spoke out after Fulham recently suffered a 1-0 loss at Manchester United, where Danny Murphy was bundled over a minute from time but 27-year-old referee Michael Oliver waved away the penalty claims.
In a statement on the club's official website, Al Fayed said: "The FA's problem in addressing this pivotal situation is that it has too much power.
"Where else can decision-makers (referees) escape all responsibility to admit serious and blatant errors and have the protesters (the football clubs involved) fined on charges of misconduct?
"The losses that we incur from such careless decisions have a huge impact and can have calamitous consequences. Referees are all too easily influenced by the more powerful clubs and individual owners which calls into question the integrity of both them, and the governing body that they report to."