TPO involves a player's economic rights being owned by third-party sources and has received plenty of criticism in the game.
Announcing the decision to launch their complaint with the European Commission, the organisations stated that often investors are concerned solely with financial return on players rather than wellbeing.
This, they said, means players "can be exposed to the whims of third parties" while "clubs can be driven into a vicious circle of debt and dependence".
The practice is commonplace in European and South American football, although FIFA confirmed its decision to ban TPO in May with UEFA and FIFPro urging the commission to endorse the move.
UEFA General Secretary Gianni Infantino said: "Third-party player ownership is a kind of modern slavery, where you see players belonging to investment funds, or other, generally unidentified, corporate entities.
"Clearly, this is not something that can be accepted by European law and this is precisely why we have now, together with FIFPro, asked the European Commission to investigate and to declare third-party ownership illegal."
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