Spain dramatically sacked coach Julen Lopetegui on Wednesday, just two days before the team's opening game against Portugal at the World Cup.
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.
At a severely delayed press conference at Spain's World Cup base in Krasnodar, Rubiales appeared to say he felt Lopetegui's decision to join Madrid so close to the start of the tournament "obliged" him to take drastic action.
"I am here to say that we feel obliged to sack the national team manager," said Rubiales.
Lopetegui had signed a contract extension until 2020 just last month and Rubiales is reportedly angry at only being informed of his decision to join Real minutes before the European champions made the announcement public.
Spain sporting director Fernando Hierro will take charge for the World Cup.
The former Real Madrid and Bolton Wanderers defender is in his second spell as sporting director, having returned to the role in November 2017, six years after leaving the position.
Lopetegui was appointed Spain's coach in July 2016 and never tasted defeat in the job, leading the team through 20 unbeaten games ahead of the World Cup.
La Roja were among the favourites to lift the trophy this summer but this astonishing upheaval, so close to the tournament, will surely affect the players.
There were fears his appointment could open up old divisions between the Real Madrid and Barcelona factions in the Spain squad.
For the first time since 2006, there are more players from Madrid in a Spanish squad for a major tournament, with a six-strong Real contingent and just Gerard Pique, Jordi Alba and Sergio Busquets from Barca.
However, according to reports in the Spanish media, the players tried to intervene at the last minute to prevent Rubiales sacking Lopetegui.
Agencies