Referee Graham Poll says the Football Association is undermining officials' authority after they failed to back him in a row with Chelsea last November.
Poll felt the FA should have given him more support
He is angry FA chief executive Brian Barwick did not step in after Chelsea disputed Poll's reasons for sending off John Terry in a match at Tottenham.
Poll, who retires in June, told the BBC's Inside Sport that Barwick ignored his pleas for the FA to support him.
However, Barwick said he was "very disappointed" by Poll's comments.
Poll, 43, dismissed Chelsea skipper Terry for two yellow cards in the Premiership match against Spurs at White Hart Lane, which the Blues lost 2-1.
Terry was later reported as saying Poll had changed his story over why he had been sent off.
Chelsea midfielder Frank Lampard and manager Jose Mourinho also waded into the row, amid suggestions Poll had sent Terry off to teach the Blues a lesson.
Poll said: "I pleaded 'You must sort this Brian, it's something you must do'. He chose to ignore that."
And the Tring official said he felt that Terry's position as England captain had influenced the FA.
Our standing is gradually being eroded away, so why should managers have respect for us?
"Unfortunately, in this case, John Terry was - and still is - England captain," he said.
"So they're left with the confrontation of England captain versus English referee.
"It shouldn't be that. It should be that whoever the player is, if he has done something wrong, he should be dealt with properly."
Poll said he felt frustrated because he was not allowed to speak out.
"They take us for granted and you can't speak out. If you speak out you get in trouble," he said.
Poll insisted he had no argument with Chelsea and said his dispute was with the FA.
"If you see an unruly child you don't blame the child you blame the parent," he said.
"In this instance to FA are the governing body, the custodians of the game, and it's their job to make sure their children behave themselves.
"If they are unruly they should bring them back into line.
"What clubs will do is push, see if they get away with it, push harder, push further and see how far they go before the custodians come down and say 'That's too far now'," he stated.
Speaking about managers, Poll said: "Because our standing is gradually being eroded away, why should they have respect for us?
"Because they can say whatever they want about us with no comeback."
Barwick, who was supportive of Poll after he was criticised for showing Croatia's Josip Simunic three yellow cards in a match during the 2006 World Cup, said he was disappointed with the comments.
I am extremely disappointed that Graham does not feel the system supported him
FA chief executive Brian Barwick
"I have always been fully supportive of both Graham Poll and referees in general," Barwick insisted.
"I actually spoke to Graham after the World Cup to offer him my support and my firm belief that he remained one of the best referees around. I also said so publicly and Graham Poll acknowledged this.
"Improving respect towards our match officials has been one of my priority areas ever since I became chief executive.
"I have always said referees do a very difficult job objectively, professionally and very well. Without a referee, there is no game.
"I did speak to Graham Poll at the time of the Tottenham-Chelsea Premier League game.
"I explained how the FA's disciplinary system worked, even though I am not, understandably, directly involved in individual cases and how we could not comment publicly while a case was ongoing to avoid prejudicing the outcome.
"I am extremely disappointed that Graham does not feel the system supported him.
"After all, in the case he has highlighted, John Terry was charged with improper conduct and fined by an independent commission who did say, publicly, that they were disappointed that the integrity of a referee had been called into question."
Keith Hackett, general manager of Professional Game Match Official Limited, the body which oversees refereeing, distanced himself from Poll's remarks.
Hackett said: "I am disappointed by his comments, especially in light of the commitment shown to the training and resourcing of match officials by the football authorities over recent years.
"The Premier League, FA and Football League are all an integral part of the refereeing structures in this country from top to bottom.
"Their involvement in the development of a group of professional referees has taken standards to a new level."
The Euro 2008 qualifier between Finland and Belgium on 6 June will be the last game Poll will referee.
Graham Poll's interview with Inside Sport will be shown on BBC One at 2305 BST on Monday 4 June.