A Spanish court has been investigating since June 2022 whether Rubiales committed a crime of improper management when the RFEF agreed with former Barcelona player Gerard Pique's Kosmos firm to move the tournament, a judicial source said.
Rubiales did not immediately reply to a request for comment but he has previously denied wrongdoing.
The RFEF said it was "deeply concerned" by the search of its headquarters and has offered its full cooperation. Spanish football's ruling body pledged "absolute transparency" in a statement posted on its website.
Five people have been arrested in Madrid and two in Granada in connection with the case, the Spanish Civil Guard told Reuters, without giving names or further details.
Rubiales angered Spanish football traditionalists by expanding the clash between the league champions and Copa del Rey winners to a four-team format, shifting the event from August to January and moving it outside Spain.
Saudi Arabia Switch
The RFEF in 2019 agreed on a three-year deal worth a reported 120 million euros with the Saudi sports authority to stage the competition in Saudi Arabia.
Judge Delia Rodrigo Diaz ordered new searches of the RFEF's Madrid base and Rubiales' Granada apartment as part of her investigation, the source told Reuters.
The national prosecutor's office said the probe was looking for corruption in business, improper management of assets and money laundering.
Police carried out 11 searches at unspecified locations across Spain related to the case.
As the Civil Guard and undercover agents searched the offices of the federation, the Spanish national team were practising on the adjoining pitch. Spain face Colombia on Friday in London and Brazil on Tuesday in friendly matches.
RFEF staff were barred from entering the building. Media covering the practice session and interviewing players were kept under close watch as police conducted searches that started at 09:30 and continued into the afternoon.
An RFEF source told Reuters that Rubiales' home had also been searched. Images showed Civil Guard officers emerging from a Granada city centre apartment with a cardboard box labelled 'Luis Rubiales' along with several other bags.
The investigation adds to Rubiales' legal woes after he was accused of sexual assault and coercion over his unsolicited kiss on the mouth of player Jenni Hermoso during celebrations after Spain's Women's World Cup victory last year.
Rubiales resigned as RFEF president in September and was banned by FIFA from all football activities for three years.
His turbulent reign as RFEF chief also included a shock decision to sack Spain manager Julen Lopetegui two days before the team's opening 2018 World Cup match.
