The Spanish football federation has been fined £180,940 for violating youth player transfer rules in the case involving Real Madrid and Atletico Madrid.
Real and Atletico are banned from registering players in the next two transfer windows after losing an appeal against their own punishments.
Fifa has given the Spanish FA six months to improve its transfer system.
It has strict rules restricting under-18 players moving to foreign clubs.
Fifa’s investigation concerned youth players who played for Atletico between 2007 and 2014, and Real from 2005 to 2014 with the clubs respectively fined £622,000 and £249,000 for breaching rules.