There will be no more FA Cup replays moving forward, with the Premier League putting up money in exchange.
EFL bosses now say they only agreed to the deal as they will be given additional funds.
The Premier League is set to put up to 33 million in additional funding for grassroots.
League One Peterborough owner Darragh MacAnthony was not happy with the decision.
He stated: We are now at the stage where the big boys don't even bother to notify us/talk through proper changes.
I have no idea what the Premier League or the FA are even thinking pulling this move the way its unfolded today.
If this is a sign of things to come then expect a full on fallout within English Football coming soon all caused by one faction of our game. It is time to show some minerals in how we respond to these events todayIgnoring us lower down the pyramid is not a sensible route to take going forward."