English soccer's governing body announced the move on Thursday as part of a six-year agreement with the top-flight Premier League to strengthen the domestic Cup competition.
"We have been discussing the calendar for the 2024-25 season with the Premier League and EFL for well over a year," the FA said in a statement.
"Removing Emirates FA Cup replays was discussed in the early meetings and all parties accepted that they could not continue."
The statement comes in the wake of multiple lower-league clubs criticising the move, which denies smaller clubs drawn at home to top-tier opposition the chance to earn revenue through money-spinning replays away.
"It does kick everyone in the teeth below (the top flight). There’s nothing we can do about it, apart from voice our concerns," Mark Robins (54), manager of Championship side Coventry City, said ahead of Sunday's FA Cup semi-final with Manchester United.
United manager Erik ten Hag (54) called the change "very sad for the British football culture," before adding that it was inevitable.
"It's due to the overload in the schedule and that's dictated by FIFA and UEFA," he said.
"You see there is so much overload on the players, we talk about this issue so often. And it has to stop... for top players, this is a measure that can make some space in the schedule."
League Two side Bradford City said in a statement that they understood "this decision was taken without any consultation with the EFL or its clubs, nor those at National League or grassroots level."
The FA said the new calendar was approved by the Professional Game Board, which has representatives from both the Premier League and the EFL, then by the FA Board where the National League and grassroots game was represented as well.
League One's Blackpool condemned the decision, adding that the club first became aware of the change after Thursday's announcement.
Leyton Orient CEO Mark Devlin called the move "potentially very damaging" for the English pyramid, adding their FA Cup replay at Arsenal in 2011 had accounted for 30 percent of the club's annual turnover.
"We have seen first-hand exactly how beneficial FA Cup replays can be," he said.
Several lower league clubs including AFC Wimbledon, Wigan Athletic, Notts County and Cambridge United issued statements expressing their disappointment, while Bristol Rovers called for the FA to "suspend their decision".
The scrapping of replays has also attracted political attention with the UK Prime Minister's deputy spokesperson saying the FA and the Premier League should explain their decision and "why it is in the interest of fans."
British opposition Labour party leader Keir Starmer said replays were part of the tradition of the FA Cup and "a real revenue raiser" for smaller clubs.
"Small clubs are really struggling financially, they need that revenue, they deserve that revenue," he was quoted as saying by the BBC. "If they’ve gone far enough to get a replay they should have their replay."
The FA said it understood the concerns that had been expressed since the decision was announced.
"We will be sharing more details with clubs very shortly to explain the additional revenue opportunities in the early rounds," the FA added.
