A meeting of youth representatives from all 12 top clubs decided that signed players could only play in the Scottish Premier League youth development initiative, or in games organised by their clubs.
But Dundee headteachers are set to retaliate by refusing to sign the "D" and "S" forms that allow boys to play with professional clubs.
Players have been told they are not allowed to represent schools, despite a dispensation to the Scottish Schools' Football Association (SSFA) in the forthcoming Victory Shield competition against England, Northern Ireland and Wales.
An under-15 match between Dundee and Edinburgh was cancelled last weekend after 12 Dundee players pulled out. Other areas are attempting to press ahead with representative games.
The clubs' tough action is designed to limit the number of games boys play.
They also want more consistency of coaching. But teachers argue that clubs overlook the importance of school activities. Rangers, for example, run three-hour training sessions for boys four nights a week and it is feared that academic work will suffer.
The SSFA points out that only a small proportion of boys signed on "D" (development) or "S" (schoolboy) forms make it into the professional game and may have no qualifications to fall back on.
The association has written to schools' representatives to urge them to reassure parents of boys signed by clubs and also those likely to attract the attention of clubs that they can still play for their school. However, boys would then run the risk of being dropped by a professional club.
It is feared that if the best players cannot join school sides it could have a detrimental effect on the grass-roots game, particularly in small communities. John Watson, SSFA general secretary, is still hopeful that the tug-of-war can be resolved as there are a significant number of players affected.
"There are over 700 boys on "D" forms at Scottish clubs at the moment. How many are with Scottish Premier League clubs is difficult to say but I should imagine it is a good proportion of them," Mr Watson said.
"I don't believe that this cannot be resolved by the schools and the clubs talking this over. It has worked perfectly well in the past. We need to get this resolved quickly - if we don't, the whole system falls away."
Niall Joss, Dundee's education spokesman, said: "We would be disappointed if this rule was enforced by Scottish Premier League clubs. There has always been goodwill between clubs and schools, and this decision could have a seriously detrimental effect on organised schools football."