The incident occurred on Sunday at Mexico's 2-2 draw against Portugal in Kazan, FIFA said in a statement, just days after it announced stricter measures to crack down on fans' behaviour at the tournament including allowing referees to stop matches.
FIFA said its disciplinary committee chairman, Anin Yeboah, had warned "the Mexican Football Federation for the misconduct of a small group of Mexican fans in relation to insulting and discriminatory chants" and said it could take further action in the event of another similar incident.
It gave no details on what action could be taken.
FIFA has already fined Mexico for fans' homophobic chants during its qualifying campaign for the 2018 World Cup.
Mexican players last year launched their own campaign against homophobic slurs during matches.
Mexico face New Zealand on Wednesday in Sochi in their second Confederations Cup match.
(Reporting by Moscow Newsroom; Editing by Louise Ireland)
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