Rubiales, who has denied any wrongdoing, arrived in Madrid on a flight from the Dominican Republic, where he had spent two months on what he described as a business trip.
His lawyer Margarita Crespo said Rubiales was asked to accompany officers to a police station, where they read him his rights, took his fingerprints and searched his belongings.
The attorney added, however, that Rubiales was not notified of anything and allowed to leave without any restrictions.
Police did not respond to requests for comment.
While Rubiales was abroad, a Spanish judge ordered searches of offices and properties linked to a probe into alleged corruption, improper management and money laundering during his tenure as president of the RFEF.
A Madrid 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 relocate the Spanish Super Cup to Saudi Arabia in a deal worth a reported 120 million euros ($129 million).
Police had searched the RFEF's headquarters outside Madrid and Rubiales' apartment in the southern Spanish city of Granada on March 20, as well as a soccer stadium in Seville. Seven people have been arrested so far.
In a La Sexta interview to be broadcast later on Wednesday, Rubiales denied accepting bribes and said his earnings were a product of his work and savings, according to promotional material released by the network.
Rubiales also confirmed Spanish police had searched his temporary lodgings in the Dominican Republic on Monday, seizing a mobile phone.
In September, he resigned as RFEF president and a month later was banned by FIFA from all football activities for three years for allegedly kissing player Jenni Hermoso on the lips without consent after Spain's women's World Cup triumph.
Rubiales argued it was consensual and has denied any wrongdoing but prosecutors are seeking a 2-1/2-year prison sentence after charging him with sexual assault and coercion.
