"Assuming the reports are correct, FFA does not condone homophobia or any antisocial behaviour. It is also important to note that reports indicate this was four people who were allegedly doing something unacceptable ... there were more than six thousand Australian fans in the stadium," an FFA spokesman said.
FFA were on Friday making every effort to speak to FIFA regarding the warning.
FFA said CEO David Gallop had not been notified of the warning and nor had FFA's head of delegation to Russia, senior counsel (who sits on the FIFA disciplinary committee), Socceroos team manager, head of international affairs or head of legal.
The Mexican football association was also cautioned after a large number of fans were caught singing homophobic chants during their win over Mexico. FIFA fined them a US$10,000.
The Australian warning was not made public by FIFA because it was only a low level incident, however FFA maintain they knew nothing of the caution FIFA claim to have handed them.