According to Spanish media the operation is part of a court investigation into contracts signed by former federation chief Rubiales to take the Spanish Super Cup to Saudi Arabia, AFP reported.
The contracts signed are worth 40 million euros a year ($43.3 million) and were arranged with former footballer Gerard Pique's company Kosmos acting as an intermediary.
The operation involved searches of various locations across Spain as well as the RFEF's base in Las Rozas, on the edge of Madrid, and Rubiales' property in Granada, although the 46-year-old is currently outside of Spain.
"I am absolutely surprised by all this," Rubiales told a journalist from Spanish television channel Telecinco.
"I have been working here for months in the Dominican Republic, I've been here for over a month straight, and in fact, my family was going to come and spend Easter with me."
Rubiales stepped down in disgrace in September after forcibly kissing Women's World Cup star Jenni Hermoso to provoke worldwide outrage, following Spain's triumph in the Sydney final in August.
A Spanish judge said in January Rubiales will face trial over the incident.
The police searches across 11 locations were part of "an investigation linked to presumed crimes linked with corruption in business, fraudulent administration and money laundering", said judicial sources.
Sources said four arrests have been made so far, including the federation's external legal advisor Tomas Gonzalez Cueto, and two RFEF directors.
"The RFEF has today offered its full cooperation to the police investigation, as well as to the public prosecutor, after the search of its headquarters," the Spanish federation said in a statement.
"Furthermore, the RFEF has called for total transparency in the institution that runs Spanish football."
"As such, it is keen that the investigation underway should proceed uninhibited until its conclusion," the RFEF added, citing its "deep concern".
Police have also searched Seville's La Cartuja stadium, where the Copa del Rey final will be held on April 6.
Spanish media said no arrests were made at the federation's headquarters, where the Spanish national team is currently based ahead of upcoming friendlies against Colombia on Friday in England and Brazil on next Tuesday in Madrid.
"I had no idea about (the police operation), we trained as normal," said Spain and Arsenal goalkeeper David Raya.
The Spanish Super Cup took place for the first time in Saudi Arabia in 2020.
After the following edition returned to Spain because of the Covid-19 pandemic, the subsequent three competitions were back in Saudi Arabia.
Spanish prosecutors opened a probe in 2022 into the Super Cup deal after audio recordings between Rubiales and Pique were leaked in which they spoke of multi-millions value commissions.
Rubiales has always defended the legality of the deal to take the Super Cup to the oil-rich Gulf state.
"If there is any type of commission, Kosmos will get it from Saudi Arabia -- the federation has not paid, is not paying and will not pay a single euro in commission to anyone for this deal," Rubiales said in 2022.
Former Barcelona and Spain defender Pique said in April 2022 "everything is legal" and that he was "proud" of the deal.
The defender twice played in Spanish Super Cups in Saudi Arabia with Barcelona before he retired from football in November 2022.
