Luis Rubiales, the president of the Spanish Football Federation, reportedly found out about Lopetegui's decision just 15 minutes before Madrid's official club announcement, and chose to go in a different direction managerially.
"We thank Julen for everything that he has done, because he is a great person, who is responsible for us being in Russian Federation", the head of the RFEF, Luis Rubiales, said. "There's a way to act that needs to be fulfilled".
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"I very much admire Julen and respect him greatly. I would have liked Rubiales to have done things in a different way".
"We have been forced to do without Lopetegui".
Real Madrid and Spain captain Sergio Ramos is said to have pleaded to have the manager who performed so well during qualifying stay on, but his departure was announced at a press conference this morning.
The former defender, who last month signed a new contract through to 2020 with Spain, spent three years with Real as a player.
"The key is to change as little as possible".
But in a staunch defence of their conduct, Pérez insisted that Madrid had acted clearly and transparently and expressed his surprise that Rubiales had taken such drastic action.
Almost 30 years ago, MI faced nearly the same situation as Spain when coach Bill Frieder announced before the NCAA tournament that he would leave after the season to take over Arizona State.
"I know there's going to be criticism whatever I do", said Rubiales. I'm sure this will, over time, make us stronger.
Lopetegui was announced as the new Real Madrid boss on Tuesday, taking over from departed Zinedine Zidane after the tournament. Spain will take on Euro 2016 winners Portugal in what promises to be one of the ties of the group stages.