Critics say the SFA-run Youth Development Initiative is failing in its aim of finding Scotland's top young talent and is also unfair in stopping young players being in their school teams.
Scott Robertson, who coaches for Musselburgh Grammar School and amateur club Musselburgh Windsor, said professional clubs tried to recruit boys as young as eight or nine and were able to sign them at 11.
But he argued the scheme was counter-productive because it restricted the youngsters' freedom to enjoy their game.
He said: "Kids who play for a pro-youth club are banned from taking part in school football. They say it's because they could get injured, but youngsters should be able to decide to play with their friends.
"School football is more relaxed and more about enjoying the game – a chance to try a few tricks, which you wouldn't dare do if you were playing for one of the initiative teams."
Over the years, Mr Robertson has helped coach stars such Kenny Miller, Colin Nish, Darren Fletcher, Steven Whittaker and Kevin Thomson.
Now he and other critics of the initiative scheme have collected more than 1,100 signatures on a petition to the Scottish Parliament calling on the Scottish Government to look at professional clubs entering into contracts with children under 16.
He said: "Taking the best players and coaches and giving them the best training should produce the best players, but it has grown arms and legs and has become a mass enterprise – we have 30 academies and 2,500 kids involved in the system.
"We should be reducing the numbers."
Justice secretaru Kenny MacAskill, MSP for Edinburgh East & Musselburgh, was due to give his backing to Mr Robertson's plea when it went before the parliament's petitions committee this afternoon.
Mr McAskill said: "I know how much Scott Robertson and other people at youth football clubs put their heart and soul into the game. We have to recognise the future of Scottish football is bottom up."
The SFA declined to comment.