The World Players' Union believes the current regulations on transfers leads to players' rights being "systemically disrespected".
FIFPro has put together what it describes as a "strategic plan to address the freedom of movement of workers within the EU, competition law and human rights" aimed at addressing the problem.
Among the rules that the organisation wants to challenge are "exorbitant" compensation packages and sporting sanctions involved in breaches and renewals of contracts respectively.
FIFPro president Philippe Piat said in a statement: "The transfer system fails 99 per cent of players around the world, it fails football as an industry and it fails the world's most beloved game.
"Football's governing bodies, clubs and leagues claim the transfer system is necessary to ensure competitive balance, whereby in fact it creates a spiral of economic and sporting imbalance, which only benefits the richest one per cent of clubs and player agents.
"Football players are workers and only when they are able to enjoy the rights enshrined in law and enjoyed by all other workers, will FIFPro be satisfied."
The organisation confirmed it will take the challenge to the European Commission, the European Court of Justice and human rights courts if necessary.
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