SFA chief executive Gordon Smith is keen to get youngsters involved
Ross County, Dunfermline and Dundee have been expelled from the elite level of the SFA's Youth Football initiative.
County and the Pars failed to meet an SFA rule asking that staff disclosure forms, relating to child protection, be renewed every three years.
Dundee did not meet the requirement of having a second youth licence holder.
County are furious and are considering legal action to contest what they argue is overly severe punishment for an administrative oversight.
Under the Scottish Youth Football Initiative Programme, clubs either play as a performance club which is where all SPL clubs are currently found, or in the initiative league.
This is a carve up. We will take this all the way
Roy McGregor Ross County chairman
The decision means only one non-SPL club, Stenhousemuir, is still able to play in the top youth league.
Dundee, Ross County and Dunfermline, who now stand to lose as much as �30,000-a-year in SFA grants, would be allowed to turn out in the initiative league.
The Fife club are considering scrapping their entire youth system as a result.
But Ross County chairman Roy McGregor told BBC Sport: "We will take this to the highest courts in the land.
"This is a carve up. We will take this all the way."
SFA chief executive Gordon Smith admitted to BBC Sport that the three clubs comply with the law of the land, relating to child protection.
They haven't met with SFA regulations but no argument was given to explain why the clubs simply were not given extra time to make the necessary adjustments.
Dunfermline say they had their staff vetted under the disclosure legislation but had been unaware of the SFA requirement to renew the disclosure forms every three years.
They told BBC Sport they corrected this within two days of being told about the problem and that they meet all the criteria required by law.
Dundee have Gordon Wallace and John Holt in place with youth licences and say the problem in their case arose due to staff moving to new jobs.
Dundee chief executive Dave Mckinnon told BBC Sport: "Last year, we had a shortfall of around �100,000 between money from the SFA and the cost of running our youth set up.
"If things go on like this, soon only the SPL sides will be able to run them."
BBC Scotland has learned that the vote to expel the youth teams was made after an investigation by the SFA professional football committee.
The four-man emergency committee comprised SFA chief executive Smith, SFL vice president Brown McMaster, SPL chairman Lex Gold and SFA president Peat.
The decision to expel two of the three clubs was unanimous. Peat used his casting vote to expel the third club after the vote was split evenly at two apiece.
Bookmark with:
What are these?