Under FIFA rules, the club where a player began his career is supposed to receive a percentage of the fee every time he is subsequently involved in an international transfer.
Many of the world's top players began their careers at small clubs where even a few thousand dollars could be useful.
However, poor record-keeping and the fact that payments are not automatic meant that clubs often missed out. Another problem is that the amounts have not changed since 2001.
"There is around $300 million that somehow has not made it to the clubs who have trained the players," Kimberly Morris, a FIFA official who oversees the transfer system, said during a football law conference on Friday.
"We know the system is too complicated, we know there is a poor record of the history of many players."
The head of the umbrella organisation for Cameroon's first division clubs told the conference that payments could often take years.
"Procedures are too long and there is no penalty when payment is late," said Franck Happi. "We can wait two years to receive 5,000 euros."
FIFA are currently working on wide-ranging reforms to the transfer system and have said that one of the aims is to improve so-called training compensation and solidarity payments.
The policy-making FIFA Council has already approved the creation of a clearing house to process international transfers.
It says this will centralise and simplify the payments associated with transfers such as solidarity, training compensation, agents’ commissions.
Giancarlo Dapoto, FIFA's head of professional football, said the amount paid in training compensation was dwarfed by the money paid in agents' fees.
Last year, US$548 million (A$767.14 million) was paid on agents commission from international transfers, compared to US$90 million (A$125.99 million) to clubs in training compensation, he said.
"There are issues with the current system that needs to be renewed to find a simpler framework and ensure the mechanism is effective," he said.
