Photographs posted on Twitter showed Meireles gesturing with his fingers behind Serbian referee Milorad Mazic's back during the first half of Germany's 4-0 Group G win.
"The Portuguese football federation (FPF) reiterates that there was no gesture directed to the match referee and regrets the speculation which would seriously damage the interests of the player and the national team," they said a statement.
"The FPF clarifies that the gesture, which has been misinterpreted, was directed at team mate Bruno Alves and merely indicated instructions from coach Paulo Bento,” the statement stated,
"Raul Meireles was just explaining that he would drop back to the position of central defender, playing on the right of the defence."
The incident occurred after Portugal defender Pepe was shown the red card in the first half of Monday's game.
Pepe leaned into Germany striker Thomas Mueller with his head, making contact and applying pressure in a needless altercation that could bring him a stiff punishment.   

Germany dismantles Ronaldo's Portugal
Thomas Mueller scored tournament's first hat-trick in Germany's 4-0 rout of Portugal in a characteristic display of attacking football even as the hitherto free-scoring World Cup saw its first drawn match on the fifth day.
Three-time champions Germany celebrated their record 100th World Cup match, the most for any country, in style by steamrolling Cristiano Ronaldo-led Portugal who played for nearly an hour with 10 men after defender Pepe was sent off for attempting a head-butt on Mueller in the 37th minute.
Mueller led a brilliant attacking brand of football with goals in the 12th, 45+1 and 78th minutes while defender Mats Hummels scored the other one in the 32nd minute.
The Group G match at Arena Fonte Nova here, however, did not live up to the pre-game hype of a marquee clash with Germany toying with their opponents and then Pepe's dismissal making it worse for Portugal.
Ballon d'Or winner Ronaldo, who made it to Portugal starting line-up after being bothered by a left-knee injury in the build-up, made little impact on the game. He threatened early with a shot from a break that Germany goalkeeper Manuel Neuer could only block. His other significant involvement was a fine free kick late into the match but Neuer was upto the task.
Germany are now joined by United States on top of the so-called Group of Death after the Americans beat Ghana 2-1 at Natal. US thus avenged their defeat against Ghana in the 2010 World Cup in South Africa in the round of 16.


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