An extraordinary general meeting of the FFA congress saw members back a new constitution by eight votes to two which will see a massive overhaul of the way football is run in this country.

Instead of power being solely in the hands of the state federations - usually working to the direction of the FFA executives - it will now be shared between federations, A-League clubs, players and women's football, with a pathway for other groups, like fans, to get representation on congress in the future.

The EGM also voted unanimously to set up a new A-League body to run the competition independently of the FFA in return for paying the FFA an annual fee.

The vote brought an end to three years of turmoil which could have seen Australia suspended by FIFA, meaning the Socceroos could have missed defending their crown at the Asian Cup and the Matildas missing out on their World Cup spot in France next year.

Instead the FIFA-approved revolution will begin to be put into place almost immediately. Nominations for the board will become open later this month, with elections to follow in November.

The new A-League v2.0 will be in place in time for next season, and a decision on A-League expansion is likely to be delayed for the moment.

But outgoing chairman Lowy - who took over from his father Frank three years ago - didn't go quietly this afternoon, and delivered a 30 minute broadside against the new regime.

He insisted the previous board and set up had retained complete independence which would be lost under the new system.

He fears the professional clubs only need the support of a minority of state federations to bring in their own people onto the board and into power.

But he did admit the status quo was no longer viable after 15 years and change was required... but said the new changes were going too far.

"I hope for the best but clearly I fear for the worst," Lowy said after the vote. "We believe the loser today is the principle of independent governance.

"This is an issue that the FFA board has been fighting for all through this. It has had a set of principles that it stuck to and it stuck to those principles, up until the last minute."

He added: "I understand why a number of the members were fatigued through the process and the ongoing debate, but it certainly was a debate worth having.

"It's a principle worth fighting for, right down to the wire. The implication of today's decisions will be played out over time.

"And we will have to see exactly how it does play out and over what period of time."

Lowy highlighted the successes of the board under the old FFA, including taking the Socceroos to four World Cup, elevating women's football and a record TV deal for the A-League.

But he added: "I don't need to revisit my fears for the game today. They are clearly well-known to you.

"Suffice to say that our game today has crossed a red line, from a corporate governance model for football to one with stakeholders where vested interests will compete for power and resources, as opposed to these being decided by independent members of the board.

"As I said a few weeks ago, this is a governance regime that I choose not to serve on. And I reiterate that I will not offer myself for re-election at the upcoming AGM."

Although Lowy said he would not be standing for re-election as chairman, he said a decision of the future of other board members had yet to be made.

But he threw his weight behind David Gallop continuing in his role as FFA CEO.

"David Gallop is one of the most experienced and best sports administrators in the country," said Lowy. "David has a contract which runs for a period of time.

"We hope deeply that David chooses to do that and then the board chooses to work with David and his senior team.

"I have enormous experience in the international business world with Westfield and seen executives around the world and I would put David  and his senior team right up there with the best."