First vice-president of the federation, Seyi Akinwunmi, is concerned that it has become a source of distraction for the players.
Team officials at the Eagles’ base camp in Essentuki have been told to address the issue ahead of Friday’s crucial clash against Iceland.
Some players were trolled on social media after Nigeria lost 2-0 to Croatia last Saturday and got involved in nasty exchanges with the fans.
“Personally, I don’t think that our players should react to people on Social Media,” Akinwunmi told journalists in Saint Petersburg on Tuesday.
“To the best of my knowledge, the issue has been addressed by those with the team in Essentuki (team base camp) and there’s no issue about that anymore.”