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 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.
"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.
"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.
- Sports & Recreation
- Milorad Mazic
- Bruno Alves