Spanish football association (RFEF) vice president Andreu Subies was arrested on Tuesday morning as part of a police operation that previously included former president Angel Maria Villar resigning on corruption charges.
Subies, the former president of the Catalan Football Federation (FCF), joined the RFEF in May after Luis Rubiales was appointed president.
"Subies has been detained as part of an active investigation into the diversion of money from the Catalan Football Federation to private ends," a police spokesman told Reuters.
Along with Subies, an unnamed second member of the FCF was arrested on Tuesday as part of the operation.
"The RFEF expresses the utmost respect for the legal actions following the events that took place this morning," the organisation said in a statement. "[We] want to highlight the necessary respect for the presumption of innocence."
Villar, who was a high-ranking FIFA official, was suspended from his role as RFEF president in July 2017 before being sacked from a role he had for nearly three decades five months later.