The Premier League is worried that Greg Dyke's plan for a B team league would "decimate" the English football pyramid.
The England Commission, led by Football Association chairman Dyke, laid out its plans for the future of the national game at Wembley on Thursday.
One of the commission's proposals is to insert a new tier into the football pyramid below League Two and the Conference.
'League Three', as it has become known, would contain a mix of non-league sides and Premier League B teams.
The idea behind the league is that it would allow young players at England's top clubs to play competitive football, rather than academy matches.
Many top-flight managers have backed the proposal, but Premier League chief executive Richard Scudamore thinks 'League Three' would be a bad idea.
"I've been on record very recently as saying the English pyramid is one of our unique strengths and would like to think we would be able to come up with a solution, which doesn't mean the decimation, the infiltration or the damage of something precious," Scudamore told Sky Sports News.
"I have some real concerns that we shouldn't be looking to infiltrate and damage the pyramid, and therefore I would like to think we should exhaust all other options and ideas."
According to the commission's report, 32 per cent of starters qualified to play for England in the 2012-13 Premier League season.
Twenty years ago, that figure stood at 69 per cent. The commission now wants the number of English players in the Premier League to rise to 45 per cent over the next eight years.
The creation of a B team league has infuriated some chairmen of lower league and non-league teams.
"It will destroy the whole fabric of the league structure," Portsmouth chief executive Mark Catlin told the BBC.
Former Leeds and England manager Howard Wilkinson, who sat on the commission, thinks the critics will come around eventually though.
"I understand their concerns fully and over time it will need to be shown to them that the positives outweigh the negatives," Wilkinson told Press Association Sport.
"When the Premier League came in there was a furore for four months about what impact that would have and look where they are now. Those who are in it are very happy."
There was a backlash from some fans.
Nearly 20,000 people signed a petition against plans for League Three within 24 hours of Dyke's proposals being launched.
The petition was started by 21-year-old Grimsby fan Lewis Horwell, who said Dyke's plans would "ruin years of tradition" if implemented.
Many Premier League managers backed the initiative on Friday, however.
Liverpool boss Brendan Rodgers, who spent much of his early coaching career overseeing youth development at Reading and Chelsea, told talkSPORT: "It's something that I've thought for years that should happen. It's something I'm a big advocate of.
"I've worked in development for nearly 15 years and I look at the investment; there's a huge investment that's been put into young players in this country, and there's a huge investment that's been put into coaching.
"The under-21s (league) doesn't bring the competition, the competitive nature, that's required for you as a manager to assess a young player.
"People will always talk about the tradition of the game here in this country, but one of the things that's most constant is change and you have to look at ways in which you can be better and giving young players a chance."
Ryan Giggs, the most-decorated player in the history of the English game, came through the youth ranks at Manchester United along with the likes of Paul Scholes, David Beckham and Gary Neville.
The Welshman, now interim player-manager at United, also gave his backing to the idea of a B team league.
He said: "I would support it.
"I remember playing at Old Trafford for the reserves when I was 15 or 16 against Everton.
"I was playing against men and it helped me. It helped you physically, mentally and it definitely brought me on.
"Rather than playing against players of their own age when it is all about technical ability, which is obviously important, you would be coming up against men at an early age and that would prepare you for what is the fastest and quickest and strongest league in the world."
Source: PA
