The figures, reported in local media and confirmed by FA, come despite record revenue of almost $140 million. The loss is almost double the $8.5 million deficit posted for 2024.
On Tuesday, FA chief executive Martin Kugeler had told Australian media that the governing body may shed a fifth of its staff to "live within (their) means".
"Increasing losses year-on-year is obviously not a situation that is sustainable or acceptable," Kugeler said.
FA said on Tuesday it had settled its long-running dispute with Australian Professional Leagues, which runs the A-League Men and A-League Women competitions.
The dispute centred on historic debts between the two organisations.
Australia co-hosted the Women's World Cup with New Zealand in 2023 and the Women's Asian Cup in March.
FA touted the World Cup as a major success as huge crowds watched the games and Australia's women reached the semi-finals.
The Matildas have since emerged as a major commercial driver for FA, bringing in new sponsorship and significant match-day ticket revenue but Kugeler said FA had failed to capitalise fully on hosting the World Cup.