Angel María Villar Llona was arrested on suspicion of embezzling funds. The president of the Spanish Football Federation and his son have been held as part the corruption investigation.
The former international footballer, Villar has been president of the association since 1988. Reports that the allegations centre on the falsification of documents and skimming profits from international football matches.
His son Gorka was among a number of other people also arrested during a number of raids early on Tuesday.
Gorka Villar served as the director-general of the South American football confederation Conmebol before standing down last year.
Before standing down, he had been accused of extortion by a number of Uruguyan football clubs.
There has been no comment yet from Villar or his lawyers.