Speaking to the media, Spanish FA president Luis Rubiales expressed dissatisfaction over Lopetegui not informing the association members regarding his decision to take over the reigns as Real Madrid coach.
In a surprise announcement on Tuesday, Real Madrid named Lopetegui as their next manager to start work after the tournament in Russia, sparking outrage among the federation and Spanish fans at the timing of the announcement.
"I think Rubiales acted correctly and was looking out for the federation, which should be above any single individual", Hernandez told sports daily Marca.
"The RFEF can not stay on the margin of the contractual situation of one of its workers", he said. Maybe this is tough now, but in the end it will make us stronger.
"There's a lot to do". "I have spoken to them and I can assure you that the players and the the new coaching staff will do everything possible to lead the team as far as possible [in Russia], but it's a complicated situation". It remains very possible that the Spanish FA - known as the RFEF - will decide to terminate his employment as Spain boss, right on the brink of the World Cup. Here is why Los Blancos opted for the Spain boss just three days ahead of La Furia Roja's 2018 FIFA World Cup opener.
Spain, one of the pre-tournament favourites, also face Morocco and Iran in their group in Russian Federation. Others believe the chaos on the eve of the World Cup just made a bad situation worse.
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Ex-Spain and Madrid defender Fernando Hierro is also with the team in Russian Federation as sporting director, while former U21 boss Albert Celades was part of Lopetegui's coaching team. He is a top coach for me, which made the decision very hard.
"I do not feel betrayed because Julen has done a relentless job, but we are forced to move on this because of how things have been done".
By successfully blending talented youngsters and veterans from its golden generation, Lopetegui kept Spain unbeaten through 20 matches in charge, comfortably leading the team to the World Cup from a qualifying group that included Italy.