He has demanded a review of both refereeing practices and the decision making process.
The Egyptian businessman has written to the Football Association and Premier League seeking an immediate review, which he says is on behalf of all clubs.
Al Fayed has spoken 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.
The Cottagers chairman has been frustrated by the recent inconsistencies and errors as well as the whole operation of officiating matches, which he believes are all too readily accepted by football's governing bodies.
In a statement on the club's official website, www.fulhamfc.co.uk, 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 and calls into question the integrity of both them, and the governing body that they report to."
Al Fayed has also urged the relevant bodies to immediately embrace video technology as he believes English football is lagging behind.
"We need brave, pioneers in the Premier League, the FA and within the Premier League shareholder group," he said.
"In the past I wrote to highlight the need for the Premier League to lead the way with the introduction of video technology.
"After many years, it appears that the Premier League has admitted I was correct all along.
"It is time for the Premier League to wake up. They have been in a coma for a long time.
"Lots of clubs are suffering from such stupid decisions. Advanced technology is available and it is evidently being used in other sports.
"Once again I call for action to review the standard of officials, and the transparency of the processes by which referees are allocated to games."
Both the FA and the Premier League declined to comment on Al Fayed's views when contacted by Press Association Sport.