Wanderers' Academy have denied allegations that they are preventing boys playing for the town teams.
Officials of Bolton Schools Under 15s and Under 14s claim they are struggling this season because their best players are unavailable due to academy commitments.
But Chris Sulley, the director of Wanderers' Acedemy, says the football club has no power to prevent youngsters playing for their schools or their schools associations.
He says the players decide for themselves.
"We as an academy work in collaboration with schools and schools associations with a common sense approach towards academy players playing too many games," he explained.
"We cannot prevent players from playing for their school or association but players need to be mindful of exceeding the 24 games recommended maximum.
"The ultimate decision lies with the player."
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