In January, world football's governing body banned the Madrid clubs from participating in two consecutive transfer windows for breaching rules regarding the signing of underage non-Spanish players, similar punishment to that handed out to Barcelona in 2015.
FIFA's Disciplinary Committee ruled on Tuesday that the Spanish federation must pay 220,000 Swiss francs (180,972 pound) for breaching article 19 of their regulations on the status and transfers of players, which is designed to protect minors.
The Spanish FA have been given a further six months to regularize their "existing system within the country" and have also been issued with a "warning and a reprimand."
The decision was made based on the investigations carried out by FIFA concerning minor players who were involved with, and took part in competitions with, Atletico from 2007 until 2014 and with Real Madrid between 2005 and 2014.
Real and Atletico saw their appeals against transfer bans rejected last month by FIFA's Appeal Committee and will not be allowed to register new players until January 2018.
The Spanish Football Federation is led by Angel Maria Villar, a FIFA vice president.
(Reporting by Adriana Garcia; Editing by Peter Rutherford)
