The announcement means that the clubs, currently third and first respectively in Spain’s top division, will not be able to sign players until July 2017 once the present transfer window closes.
There were no immediate comments from the clubs, which have the right to appeal the decision.
Real’s great rivals Barcelona, standing second in La Liga, were handed the same penalty in April 2014 for also breaching rules on the transfer of under-18 players. The Barcelona ban finished with the start of the current window, which runs until the end of January.
Atletico were fined $US900,000 and 10-times European champions Real $US360,000, FIFA added.
The two clubs were given 90 days to regulate their situation but can continue to sell players.
FIFA said that “the two clubs were found to have violated several provisions concerning the international transfer and first registration of minor players.”
FIFA said the investigations concerned players who participated in competitions with the clubs between 2007 and 2014 in the case of Atletico, and between 2005 and 2014 in the case of Real Madrid.
“FIFA works hard to protect the rights of players under the age of 18 – whether male or female, amateur or professional,” said FIFA in a statement.
“This is done through the enforcement of regulations prohibiting the international transfer of minors, or the first registration of minors in a country other than their own, except in specific circumstances.”
The next two transfer windows are July/August 2016 and January 2017.
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