Reports on Thursday suggested supporters of the Central American nation were heard performing homophobic chants during their goalless draw with Brazil on Tuesday.
The global governing body stopped short of detailing the specifics of their investigation, but have confirmed they are looking into the matter.
In a statement, FIFA said. "We can confirm that we have been contacted by FARE (Football Against Racism in Europe).
"Prior to this, disciplinary proceedings were opened against Mexico for improper conduct of spectators during the match Mexico – Cameroon.
"As the proceedings are ongoing, we are not in a position to comment further."
FIFA also refuted claims there were a number of other teams under investigation.
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