RFEF president Luis Rubiales revealed the decision after a dramatic morning when a press conference was called for 9.30am and then delayed over an hour and a half.
Lopetegui was announced as the new Real Madrid manager yesterday, to take over after the World Cup, but Rubiales has confirmed he has now sacked him.
He said: “We have been forced to dispense with the national coach, we wish him the best of luck, what the Spanish gets, will have to do with the work he has developed.
“We have to work on a series of decisions that come two days before the beginning of Russia 2018. There is a lot to do.
“I do not feel betrayed, Lopetegui, while he has been with us, has done an impeccable job, another is how this has been done, without knowledge of the federation.
“We will touch the staff as little as possible, as soon as we have something to communicate, we will do it.”
Spain’s World Cup campaign is now in chaos with their first game against Portugal on Friday.
Yesterday Real Madrid announced the Spain boss would take over as their new manager following Spain’s involvement in the World Cup.
“Julen Lopetegui will be the Real Madrid coach after the celebration of the 2018 World Cup,” the Real Madrid statement read.
“Real Madrid C. F. announce that Julen Lopetegui will be the coach of the first team during the next three seasons.
“Julen Lopetegui will join the club after Spain’s participation in the World Cup, after two years leading the national team.”
And now the 51-year-old will be replaced a day before the tournament starts.
Rubiales is said to be fuming at the Real Madrid announcement, only learning about it 15 minutes before it was made public, after Lopetegui signed a new deal with Spain until 2020 on May 22.
But now it is being reported that the players – lef by Sergio Ramos – wanted him to stay.
Spanish football expert Guillem Balague tweeted: “President of Federation, Luis Rubiales, preferred his sacking from the moment he heard Lopetegui was the new RM manager only minutes before the official confirmation yesterday. His position won the debate with players.”
Spain are among the favourites for the tournament but face a huge task should Lopetegui go.
It is being claimed the most likely candidates to replace him are Under 21 manager Albert Celades or Fernando Hierro.
Spain open their campaign on Friday against Portgual before facing Iran and Morocco.
The press in Spain were split on the decision to make the announcement of the appointment now.
Spanish newspaper SPORT branded the appointment as ‘reprehensible’.
“The consequences of it can be disastrous for the Spanish team,” wrote Lluis Miguelsanz.
“What is clear is that Lopetegui has been negotiating his future as the new Los Blancos coach while preparing for the World Cup, something that is ethically already reprehensible.
“There is no doubt that the coach has all the right in the world to train whoever he wants, but his standing is questioned by the proximity of the start of the competition.
“The situation demands immediate explanations.”
Spanish newspaper Marca, meanwhile, appeared to defend Real for their appointment and dampened down worries over its timing.
Marca, known to be a Real mouthpiece, published: “That it was not the ideal moment is evident … but it is also true that circumstances have determined this outcome.”
They added: “It is clear that the arrival of coach Julen to Madrid has not been done at the most opportune time for the national team.
“But with the professionalism and commitment of all, the squad should not be affected. Surely it is like that.”