Sir Trevor Brooking says youth development in English football is suffering from inadequate regulation, short-sightedness and outdated methods.
Young English talent is finding it harder and harder to get noticed
The FA's director of development said it was his goal to make the decision to buy foreign players a "tougher one" but he was being prevented from doing so.
Speaking to BBC1's Inside Sport, Brooking said the English game faced "huge challenges" at every age level.
And he called for the governing body to be given more power to force change.
Brooking was handed control of the FA's coaching network almost four years ago but has grown increasingly frustrated by his inability to persuade the professional game to agree a new, unified plan for player development or even ensure that the existing one is being properly implemented.
The 58-year-old England and West Ham great likened the current regulatory system to being "a bit like marking your own exam papers at school".
"We identified half a dozen academies 21 months ago and asked (the Football League and Premier League) for permission to work with them and raise the standard," he continued.
"But that permission was refused and that's when we got to the situation when no one has the power to do anything.
We need to decide what is the one plan we should use to develop youngsters so that when they get to the professional game they have the ingredients
"From the professional game point of view, what can we change? We can't change anything.
"And the worry is that while that just drifts along, standards are actually deteriorating.
"That's why we have concentrated on our skills coaches for grass-roots football, strengthening the coaching department within the FA and writing up our new age-appropriate courses, which we strongly think are the way to go.
"We will roll those out at the beginning of next year and would like the professional game to buy into them but that's for them to decide. I can't make that decision for them."
The current structure of academies and centres of excellence, which was set up by Howard Wilkinson in 1997, has come in for considerable criticism in recent years.
Many managers and owners have bemoaned the poor returns on investment that the academies have produced and others have suggested they are little more than public relations exercises to placate fans' desire for home-grown heroes.
Premier League clubs fund their own youth set-ups, and the vast majority have full-blown academies, while Football League clubs receive a grant of £138,000 for their programmes from a central fund provided by the Football Association and the Premier League.
The entire system has been the focus of a recent review led by Rugby League chairman Richard Lewis but key decisions on how the academies are funded and regulated have been postponed.
"It's frustrating," said Brooking. "It's frustrating for a lot of good quality coaches working in the clubs.
"They would like us all to work together and go forward. There's a lot of agreement on what should be happening."
The former midfielder turned administrator has repeatedly called for Wilkinson's 1997 Charter for Quality to be revamped to reflect current thinking on coaching and sports science.
He also wants to tidy up some of the ambiguities in the system. For example, academies only have to provide "adequate facilities" - Brooking describes "adequate" as a "very flexible word".
And he would like to be able to financially reward "good" academies and punish failing ones.
Brooking is concerned about the supply line to the national team
But most of all Brooking wants the FA to be given the power to monitor the entire youth development system and spread best practice and the latest methods from those who can afford to them to those who cannot. To do this he is advocating the creation of a "pro game unit".
This new body, with financial and regulatory muscle, would also help balance the growing influence of foreign owners in the English game.
"Whatever investment we have we should ring-fence the money and invest it," he said.
"In other countries that is where the national governing body takes a big lead as they are the only body that has to look long term.
"We have to think about the future and benefit of the game. But in most countries the governing body works with the professional game and I'm convinced that we have to work together.
"We need to decide what is the one, unified plan we should use to develop youngsters from five to 16 so that when they get to the professional game they have the basic ingredients.
"We must agree the content, the courses, the quality assurance, the child protection issues, the accountability measures and so on, and make sure everybody works to the same plan.
"At the moment that is a long way off."