The German boss has drawn criticism for announcing that neither he nor his first-team players will be present for the fourth-round replay at home to Shrewsbury next week as it falls within their scheduled Premier League break.
Instead, the club will send out a youth team led by Under-23s coach Neil Critchley.
"If we react how we always react and find a way to do it, then nothing will change," Klopp said. "I have to make decisions that aren't popular, based on the situation we are in.
"Because we plan long-term I cannot plan when there is a real decisive period coming up. I decided three weeks ago we would have a mid-season break based on a letter we got in April 2019.
"The FA tried to move games to midweek to decrease the intense period. Whoever was involved in that -- maybe from us -- they forgot to say no."
Liverpool, who play West Ham in the Premier League on Wednesday, are closing in on their first English top-flight title for 30 years and are also through to the last 16 of the Champions League.
A Liverpool side led by Critchley lost 5-0 to Aston Villa in the League Cup quarter-final in December while the first team competed in the Club World Cup in Qatar, a competition they went on to win.
Manchester United boss Ole Gunnar Solskjaer said he could understand Klopp's frustration and still regrets United's decision to pull out of the competition 20 years ago.
Solskjaer, whose side beat Tranmere 6-0 on Sunday to progress to the fifth round of the FA Cup, was part of the United squad that pulled out of the tournament in 2000 to play in the FIFA Club World Championship.
"I think we all regret maybe not going for it in 2000, when we went to the World Club tournament in Brazil and it's never nice not to be participating," said the United boss.
"It's supposed to be a break and if we're going to help the English clubs, they need a break.
"But that's up to Jurgen and Liverpool to make decisions. Jose (Mourinho) and Tottenham, they've got a replay. We're just happy we didn't get a replay ourselves because it was playing on our mind."
Manchester City boss Pep Guardiola supported Klopp's stance, saying: "We accept the schedules and the competitions, games every two or three days, but don't tell the managers which players to pick."
Klopp said forward Sadio Mane would likely only miss another two matches after tearing a muscle in last week's match against Wolves.
"Sadio will not be involved for West Ham and probably not Southampton," said the Liverpool boss.
"After that he will be back on track. He has a small muscle tear which is serious enough. We were lucky with it, though, it wasn't too serious."