Angel María Villar Llona, a former soccer player, was arrested on suspicion of embezzling funds, El Pais and Efe news agency reported.
He has been president of the association since 1988.
His son, Gorka Villar, was among a number of other people also arrested during a number of raids on July 18.
Spain’s High Court told Reuters that one of its investigating magistrates and anti-corruption prosecutors were leading the probe.
Spanish media report that the allegations centre on the falsification of documents and skimming profits from international soccer matches.
There has been no comment yet from Angel María Villar, 67, or his lawyers.
In his time as president of the federation, Spain’s men’s soccer team has won two European championships as well as the 2010 World Cup, becoming one of soccer’s dominant forces.
Angel María Villar has also served on the council of soccer’s world governing body FIFA for the past 29 years, but was reprimanded by FIFA for failing to comply with its internal inquiry into the 2018/22 World Cup bidding process.
He was acting president of UEFA, Europe’s soccer association, while its chief Michel Platini was under investigation. He lost out on the presidency in an election last year.
UEFA and FIFA said they were aware of the reports.
Gorka Villar served as the director-general of the South American soccer confederation CONMEBOL before standing down last year.
Before standing down, Gorka Villar had been accused of extortion by a number of Uruguayan soccer clubs.
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