Australia - known as the Matildas - lost 3-0 to England on Friday at the 2015 Cyprus Cup - an invitational international tournament.
But the result was overshadowed by reports - first made by English football blog Girls on the Ball - that British soldiers had allegedly made sexist comments towards the Australian players.
In a statement, the FFA confirmed "inappropriate comments" had been made but appeared to indicate they consider the incident dealt with, after an apology was made following the match.
"FFA can confirm there was inappropriate comments directed at players and match officials from members of the UK Military who were watching the Matildas play England at the Cyprus Cup," an FFA spokesperson said.
"A senior officer from the Military group offered an apology to the Matilda's management as soon as the match finished and that apology was accepted.
"FFA condemns the sexist and anti-social behaviour on display at the Cyprus Cup and reaffirms our position of zero tolerance, as contained in FFA's National Code of Conduct."
The British media have widely reported that both the Football Association and Ministry of Defence will investigate the claims.
