Premier League chief executive Richard Scudamore has insisted that all relevant bodies need to preserve the pyramid of English football.
Greg Dyke's FA commission yesterday announced plans to introduce a division beneath League Two for Premier League 'B teams'.
The proposal has been met with widespread debate, but a number of top-flight managers, including Liverpool boss Brendan Rodgers, have backed the notion.
"We all understand the issue," BBC Sport quotes Scudamore as saying. "How do you take all this investment and progress in youth development, and from 18 onwards convert them into players who are capable of holding their own in the Premier League and becoming England qualified talent?
"That is the challenge we all have. I can't contradict what I have said before many times before and truly believe. I don't believe we should be interrupting or wrecking the pyramid of English football to achieve that.
"We must see if there is a credible alternative before we go decimating the Football Conference and the Football League. That is something we need to try and protect almost at all costs."
The commission have also proposed that non-homegrown players should be reduced in Premier League squads from 17 to 12 over five years, while a ban should be imposed on non-EU players to join clubs outside of the top flight.
