Holloway believes the Bosman ruling of 1995, which allows players over the age of 24 to move for free at the end of their contracts, unfairly penalises clubs.
Manchester United manager Sir Alex Ferguson this week confirmed Rooney has told the club he will not sign a new contract, meaning he can walk away for nothing when his current deal expires in the summer of 2012.
An impassioned Holloway said: "I've got big problems with the people who are running football. I know the reasons I think the game is in trouble and you cannot have a Bosman ruling they've got at the moment.
"Manchester United have helped Wayne Rooney's career massively on and off the field. The manager, the club itself has invested in him. They bought him for massive amounts of money as a young man and they're helping him blossom into the player that he is.
"He's one of the best centre-forwards in the world. And if he sees his contract out he's going to be able to walk out of there for nothing. That's the people at the very top of the game's fault.
"Our rules were brilliant. If he was offered the same amount of money again, they could hold his registration and someone would have to pay the fair amount of money for him.
"Just because you're 24, what on earth has that got to do with it? It's just ludicrous. They have the power to change this straight away.
"What if he sits there for 18 months, throws tantrums, doesn't try, doesn't play, and someone's already said to him, 'We'll take you and we'll pay you some of that money we should have paid Manchester United because you can walk out on a free'?
"Do you want to sign a person like that? Do you want to play for a club that says that to you? How do we know it hasn't already happened? The game is wrong. The people in charge of the game are wrong. They are so wrong this is frightening.
"If Alex Ferguson is being bullied by a player and his agent, how wrong is the game? When are you (FIFA and UEFA) going to listen to the people who are involved in the game?
"They say it's not fair on the player. Rubbish. The player has had his wages every week. They bought him, they worked with him, he belongs to them. It's so obvious. The world should change if it's wrong and football should look at itself.
"I'm looking at Alex Ferguson and thinking: 'What a magnificent manager. How can he handle this?' How he feels about Manchester United, how proud he is. Yet Wayne Rooney or his agent can now manufacture a situation like this."
It was Holloway's second rant about the rules of the game in a week after the Tangerines boss used his post-match press conference on Sunday to call for the introduction of video technology.
Holloway, who was serving a touchline ban and watched the game from the stand, was unhappy with a number of decisions in the 3-2 defeat by Manchester City that went against his side.
But the former Leicester and QPR chief praised Phil Dowd after revealing the referee had phoned him on Monday to discuss the decisions involved.
"The conversation I had with him, I've got so much respect for him now," said Holloway. "But, at the time, it's affected the result. I'm not against them (referees), I'm against the people who are deciding they're not allowed to use the technology."