The Brazilian and Mexican football federations could face sanctions for the "homophobic" behaviour of their fans.
Fifa have launched an inquiry after the use of the word "Puto", meaning male whore, was directed at the opposition goalkeeper during their Group A game on Tuesday in Fortaleza.
Russian and Croatian football authorities also face punishment after "neo-Nazi" banners were allegedly displayed during matches.
The Fare network, which is monitoring discriminatory behaviour at the World Cup, reported the incidents to the world governing body.
Fifa's anti-discrimination policy says a first offence can lead to having a game being played behind closed doors.
Further offences bring more serious sanctions, including points deductions, relegation or expulsion from a competition.