Two further allegations of inappropriate behaviour towards children, involving Premier League clubs, are also being investigated. The cases range from bullying to criminal offences and raise concerns about the safety of millions of young people who play football.
An 18-month investigation by the Independent Football Commission praises the progress made by the industry in protecting children, but warns that it faces a "daunting" task in preventing abuse. The commission's report was compiled with the help of the National Society for the Prevention of Cruelty to Children.
It found that some clubs did not have adequate vetting procedures, including criminal record checks, for staff who work with children.
Concerns were raised about how the names and photographs of child players and mascots often appeared in match programmes and club magazines in a way that could lead to them being identified and targeted by abusers.
Top clubs were told they needed to improve supervision of their star players when meeting young fans, particularly teenage girls.
The investigation criticised the way the FA and the Premier League conducted separate inquiries, so that someone banned by the FA could still be able to work in the Premier League.
A snapshot survey this year found that 250 allegations of abuse were being investigated by the FA, in addition to two cases which were being investigated by the Premier League.
No details of the clubs or the allegations were given in the report, although they are thought to range from relatively minor complaints about parents shouting at children on the pitch, to criminal behaviour.
Tony Pickerin, head of child protection at the FA, said it had removed up to 70 people from the game in the past five years fater criminal record checks. A licensing system for coaches and photo ID cards for those working with children were being considered.