Lopetegui was announced as Zinedine Zidane’s successor earlier this week in a move that surprised many.
The announcement initially claimed that the 51-year-old would take the reins at Santiago Bernabeu after the conclusion of the tournament, but La Roja have acted now.
“We have to decided to fire the national coach,” Spanish Football Federation president, Luis Rubiales, said. “What we have achieved in getting here is due in great part to him, and we must thank him and wish him luck.”
Rubiales insists he does not feel undermined, but has suggested that Real acted in a manner unbecoming of their status.
“I don’t feel betrayed. Lopetegui has done impeccable work. How all this has been done is something else.
“I have spoken with the players and I can guarantee they will do everything, along with the new coach, to take the team as far as possible.
“Real Madrid look for the best coach, that is fine by me. I have no opinion about how Real Madrid act. But the federation have an obligation, to represent all Spaniards.
“To win is very important, to have the best coach very important, but above everything is acting in the right way. Maybe this is tough now, but in the end it will make us stronger.”
Lopetegui was unbeaten in his time in the Spain dugout, guiding his team to 14 wins and six draws from 20 matches.
Spain face Portugal on Friday, and will also face Iran and Morocco in Group B.