The Consejo Superior de Deportes (CSD) took the decision unanimously as a "precautionary and provisional" measure, it said in a statement, adding that the decision could be reversed depending on how the situation develops.
Villar, a former Athletic Bilbao and Spain midfielder, has headed the RFEF for 29 years and is a vice-president of world soccer's ruling body FIFA and Europe's UEFA.
Villar, his son Gorka and two other football federation executives were detained on July 18 on allegations of collusion, embezzlement and falsifying documents. Villar has denied all the allegations.
A judge ordered on Thursday that Villar should be remanded in custody.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Juan Padron, one of the other executives arrested, was also suspended by the CSD for one year on Tuesday.
Villar, who was in his eighth term as RFEF president and was re-elected in May when he stood unopposed, is the latest leading football official to be arrested or banned.
Since 2015, several dozen leading officials, mainly from Latin America, have been indicted in the United States on corruption-related charges.
Several have pleaded guilty and are awaiting sentencing, others have pleaded not guilty and are awaiting trial and some are in their homeland where they are fighting, or have avoided, extradition.
Meanwhile, former FIFA president Sepp Blatter has been banned for six years and former UEFA chief Michel Platini for four by FIFA's ethics committee.
Neither FIFA nor the RFEF could immediately be reached for comment.
(Writing by Brian Homewood in Berne, editing by Ed Osmond)
