A plan to introduce Premier League 'B' teams into the Football League is the headline recommendation of Football Association chairman Greg Dyke's England Commission set up to address the lack of opportunities for homegrown players at elite domestic level.
Scudamore supports the aims of the commission, but does not want it to be at the expense of the current English pyramid system.
He told Sky Sports News: "The commission report has hit upon an issue that we are all faced with - a big challenge as to how do you take this huge investment that we make in youth up to the age of 18?
"How do you get all that talent through and convert it into first-team players able to hold their own in the Premier League and able to compete for England?
"That's a challenge we recognise. We know we have to address it and we are going to sit down and yet again re-examine everything we do in terms of trying to overcome that challenge.
"So I have no issue with the identification of, if you like, 'the problem', but I have been on record very recently as saying I think the English pyramid is one of our unique strengths and I would like to think we would be able to come up with a solution which doesn't mean the decimation or the infiltration or the damage really of something precious.
"I have some real concerns we shouldn't be looking to infiltrate and damage the pyramid and therefore I would like to think we should exhaust all other options, all other ideas."
Scudamore also insists the Premier League remains "hugely supportive" of the Football Association.
He said: "The starting point is our clubs play in the FA Cup and they enjoy playing in the FA Cup and they want to win the FA Cup.
"We absolutely encourage and make sure clubs release players when they are supposed to release them for England duty and fundamentally that's the most supportive you can be."