The union that represents footballers around the world will on Friday launch a landmark legal action against Fifa in the hope of outlawing the transfer system and fundamentally changing the professional game.

Having run out of patience with Fifa and Uefa following long-running negotiations over reforms to the transfer system to protect players better, Fifpro’s lawyers will electronically file a complaint in Brussels with the European Commission.

Fifpro wants to abolish transfer fees and make it easier for players to move between clubs while respecting contracts. It believes its members have less freedom of movement than other workers when a club is able to demand a fee for a footballer under contract. Its lawyers also plan to argue that the existing system is anti-competitive because it places disproportionate power in the hands of elite clubs who can afford to pay large transfer fees.

Other Fifpro objectives include an end to the loan system, restrictions on squad sizes and the capping of payments to agents.

“Whatever happens, it is a historical moment not only for Fifpro but for professional football,” said Fifpro’s general secretary, Theo van Seggelen, who claims to represent 65,000 players across 65 countries. “We were responsible for Bosman, we were responsible for the declaration of objectives in 2001. We thought we had a good position then but we were tackled from behind.

“We’ve tried to solve this problem internally with Fifa and Uefa but I am 100% convinced that they have left us with no choice. I have been used to negotiating my whole career, with Fifpro and the Dutch union. But it has come to an end.”

Its lawyers believe it will result in the most seismic changes since the Bosman case to a transfer market they believe has become badly warped and no longer serves the best interests of players, fans or clubs. Moreover they will argue that it entrenches the dominance of the biggest clubs and damages the wider game.

“If we win this case and the European Commission declares it illegal, it will be like what happened after Bosman,” Van Seggelen told the Guardian, referring to the 1995 case that guaranteed freedom of movement for players when they reached the end of their contract.

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“They have to change it. And if they don’t do it, there will be a declaration of objectives where they have to change it by a certain deadline.”

In the complaint to the Directorate General of EU Competition, Fifpro will argue that several opt-outs from European law agreed under a 2001 settlement have not been adhered to and are no longer in the public interest. They plan to argue that the transfer system is anti-competitive and also breaches European law on restraint of trade and freedom of movement.

The Commission could take six to 12 months to reach a decision and, if it rules in favour of Fifpro, lawyers estimate that it could take one to two years of horse trading beyond that to come up with a new set of rules.

Fifpro will argue that the transfer system breeds instability, with small clubs gambling on selling one or two star players to sustain themselves.

It will also point to new research from the economist Stefan Szymanski that shows that the argument that there is a “trickle down” effect from the transfer system from the biggest to the smallest clubs no longer holds water.

“The transfer system as it currently operates is intended to achieve a number of pro-competitive benefits in football markets by placing restraints on football players,” said Szymanski. “These restraints significantly impact the economic and social wellbeing of the players both in theory and in practice.

“Even if it were possible to justify these restraints because of the wider benefit to football, there is little evidence that these wider benefits have materialised. But in reality, it remains the case that there are better alternatives to achieving the stated policy goals, as observed by Carl Otto Lenz Advocate General at the European Court of Justice in the Bosman case 20 years ago.”

Szymanski’s 20-page analysis concludes: “As it currently operates, the transfer system sustains the dominance of the elite clubs by ensuring that they are the only ones with the financial muscle to afford the transfer fees payable for the very best players. Thus, as it currently operates, the transfers system is not only unfair to players, it also promotes the opposite of what was intended.”

Facebook Twitter Pinterest Manchester City’s squad size was cited as an example of the game’s imbalance by Fifpro’s Theo van Seggelen. Photograph: Paul Ellis /AFP/Getty Images

Van Seggelen said it was difficult to be specific about what the future might look like if transfer fees were abolished. But he argued the biggest clubs had nothing to fear.

“Without a transfer system, the best players will still play at the best clubs,” he said. “The contracts will be shorter. But that’s not enough. So we also have to come up with alternatives to be sure that we will not have an unintended effect. We also need stability – you can make the contracts one, two, three or four years. You can say it will be very difficult for a club or a player to breach their contract.”

One vision of the future would provide a “protected period” where neither club nor player could break their contract within the first two or three years (unless there were extenuating circumstances where they were not getting a game). Then the player would be able to buy out the remainder of his contract and switch clubs. It would also limit contracts to a maximum of, say, four years.

If the brave new world went hand in hand with other governance reforms – capping agents’ fees, limiting squad sizes, getting rid of the loan system – Van Seggelen argued it would not remove the advantage of the biggest clubs but would stop money flowing out of the game and produce more stability.

“If the agents are going to decide where a player is going to play because a club will give him €20m, that is a problem we have to tackle,” he said. “That is why we have to put restrictions on the intermediary fees. Otherwise you will create another problem. We have already thought about that.

“You have to think about squad size limits – you can’t have a Manchester City squad with 60 players – and we have to forbid the loan system. It’s logical. And get rid of the agent fees. Those are the points we have to think about.”

He also argued that wholesale reform of the transfer system to better protect players and create more stability should go hand in hand with measures to improve competitive balance in the game across Europe.

“It’s a packet of measures – you also have to look at the distribution of money. I look at all the countries,” he said. “In Slovenia football is small. We are not in a communist situation where everyone will become equal. The product from England is fantastic. They will still have the most money. That is not the problem.”

The impasse has come about because Fifpro claims the biggest clubs wanted to link new rules around guaranteeing payment of salaries – a major issue in some smaller leagues – to concessions elsewhere.

Fifpro has maintained that new rules on “overdue payables”, ensuring that players get paid on time, should be a given and not linked to the wider negotiation over the transfer system.

A 2012 Fifpro study across 12 countries showed that 42% of players did not receive their salaries on time. Van Seggelen insisted the biggest clubs in Europe had nothing to fear from getting rid of transfer fees and that smaller clubs had plenty to gain. He argued the only losers would be the agents and middle men taking money out of the game. Fifa’s own figures show that agents’ fees on international transfers rose to £155m in 2014.

“We are not the only ones complaining about the ridiculous system with the transfer window. There is the press, the fans,” he said. “Everybody understands that you want to end the season with the same team you start with. We are not saying ridiculous things.”

The Dutch secretary general, a former player, said the landmark case was a fitting way to mark the organisation’s 50th anniversary and insisted the widespread stereotype of footballers being concerned only with their own pay packet and position was unfair.

“Top players know where a player in the second division is coming from,” he said. “They know it could have been them. The solidarity of the players is unbelievable.

“I speak with players from all over the world, from Japan to Bolivia. The only difference between players is that one has a second-hand bike and the other has a Ferrari. All the players have to sacrifice to become a professional player.

“Our top players promote Fifpro, they are happy to be in our world XI, they are happy to be treated like everyone else. That is why the top players in Spain demanded that players in the third division were paid two years ago. We represent 60,000 players and we are united.”