Atletico Madrid have not been notified by FIFA or the Spanish Football Federation that they are under investigation over the transfer of players aged under 18.
Reports in the Spanish media on Tuesday claimed that both Atletico and Real Madrid are being probed by football's world governing body and could face transfer bans.
"We have not received any notification by FIFA or by the Spanish Football Federation (RFEF) regarding the reports that are circulating in the Spanish media," Atletico press officer Juan Jose Anaut told Press Association Sport.
"We want to state that we have cooperated with FIFA at all times.
"We believe we have followed the correct steps when it comes to licencing under age players as we have followed the guidelines of the RFEF and the Madrid Football Federation just as FIFA stipulates in order for licences to be approved."
Last year, Barcelona were punished for breaching FIFA's rules on the transfer of international players aged under 18.
The Catalan giants are currently serving a 14-month ban and cannot sign players until January 2016.
Barca appealed against the punishment to FIFA and to the Court of Arbitration for Sport (CAS) but the punishment was upheld.
Source: PA
