Social media platforms were awash with an image of the midfielder appearing to raise his middle fingers towards the referee after team-mate Pepe was sent off due to an altercation with Thomas Muller.
The Real Madrid defender was dismissed after clashing with the Germany forward, who scored a hat-trick, but the Portuguese Football Federation (FPF) have denied Meireles gestured at the official.
Instead, they claim the Fenerbahce man was giving out tactical instructions to team-mate Bruno Alves as Portugal had been reduced to 10 men.
"The FPF, contrary to what was conveyed in the media and on social networks, flatly denies the athlete Raul Meireles has done any incorrect gesture following Pepe’s red card," read a statement on the body's website.
"The FPF clarifies that the gesture was misunderstood. Meireles headed to his colleague Bruno Alves and only conveyed the instructions of the coach Paulo Bento following the card.
"Raul Meireles just explained that he was moving back into central defence to play on the right side of the defensive axis."
Portugal will need to recover quickly from their humbling ahead of remaining Group G fixtures against the United States and Ghana.
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