Member associations have rejected the FFA's proposed reform of its Congress at today's Annual General Meeting in Sydney.
FIFA can now take a range of steps including the option to install a normalisation committee to govern the game in Australia until the matter is resolved.
FFA Chairman Steven Lowy did not state if the board would accept FIFA intervention meaning a legal fight could ensue over who runs the sport in Australia.
Australian Professional Football Clubs' Association (APFCA) chairman Greg Griffin said the FFA board had lost the "dressing room".
“Our position was guided by the fact that two of the three FIFA identified stakeholders, APFCA and the PFA, have identified two threshold matters that are fundamental to achieving an outcome of good governance," he said.
"They are that no single stakeholder should ever again hold a majority equal to, or greater than the prescribed majority required to elect Board Directors and that any congress reform solution must recognize the importance of gender equality in football in a meaningful way. The FFA Board’s unilateral resolutions fell far short on both matters.
“FIFA has been clear for the last 14 months about what is required. The FFA Board has continuously ignored those requirements and the ongoing direction from FIFA. What has motivated them to do so is clearly for them to answer, but they have lost focus on the ongoing needs of our game and have now lost the dressing room.”
The Professional Footballers' Australia (PFA) released a statement acknowledging the outcome.
"The PFA is not a member of FFA and accordingly did not lodge a vote as a part of the AGM process, although it was in attendance as an observer," the statement said.
"The PFA will make no further comment until it has discussed the outcome with its Executive Committee, which features current players including Sydney FC’s Alex Wilkinson, Socceroos’ captain Mile Jedinak and the Matildas’ Lydia Williams."