Last month, the FA's technical director, Howard Wilkinson proposed that professional clubs, not schools, should have sole responsibility for developing talented youngsters. And clubs, instead of the English Schools Football Association, should be in charge of the under-15s team.
Malcolm Berry, chief executive of ESFA, said: "In this country, we have a strong school football based organisation. In other countries their strength revolves around clubs. Here it is about partnership."
The council of the Secondary Head's Association has passed a resolution condemning the plan for allowing clubs to exclude top players from school football.
John Sutton, general secretary of SHA, said: "That young players would not be permitted to play at any level in schools football is high-handed, unfair and elitist."