Moore, who played for Australia at the 2006 and 2010 FIFA World Cups, said he was deeply dismayed by the poor governance that is damaging the game.
He feels football's administrators are letting down the coaches and players who collectively have lifted their game this season, saying the only solution is for the FFA to continue to govern the national teams and let the A-League be run independently.
"You've got to have a breakaway because too many people have no confidence in the FFA which tells you that change has to happen sooner rather than later," Moore said.
"Australian football is in a very delicate situation. We are at the crossroads.
"The natural progression for our game is for FFA to administer the national teams and an independent body to look after the league.
"FFA should make sure that the national teams and their programs are fully resourced and the players (are) given the best chance to fulfil their potential.
"The A-League clubs and those in the second and third tiers need an opportunity to grow the game because they are not getting it at the moment."
Moore, who is now director of football at Brisbane Roar, is deeply concerned by football's inability to build on the initial success of the A-League and the achievements of the so-called 'Golden Generation' of which he formed a major part.
He feels the current business model in which the FFA pockets the profits from the A-League finals series, while placing restrictions on the sponsors clubs can sign, only serves to hamstring the league's growth.
"The ongoing saga about the congress is a clear indication that there is unrest," Moore said.
"A lot of people are very unhappy with the direction the game in Australia is taking with FFA in control.
"You have 10 A-League clubs that have come together to fight for change. There is no opportunity as things stand for clubs to prosper.
"There are a lot of restrictions to the business model. Clubs don't benefit from the finals which are the biggest games of the season that draw the biggest gates, they don't gain enough from the sale of merchandise and they have some real issues in bringing new sponsors to the table such as car manufacturers.
"FFA are clearly under-resourced and when huge important cuts are made like closing the Centre of Excellence and cancelling a tour abroad for the Under-23s, one is entitled to feel a lack of confidence in the leaders of our game.
"There is a lot of anger within the media while those in the coal face feel a great frustration because we all want to take this game forward."
The standard of most A-League games this season has been more than satisfactory mainly due to the quality of imports but the crowds are not responding sufficiently well.
Poor promotion in the weeks leading up to the competition's kick-off is seen by many as the main reason for the fans' apathy.
Brisbane Roar's new Italian striker Massimo Maccarone has lamented the fact that he has played in big stadiums that are "always empty" in his maiden A-League campaign.
"We've been saying this for years but you don't appreciate this until you get someone like Maccarone - who has played at the highest level - saying he cannot comprehend how the game can grow when you get juniors playing for only six months a season," Moore said.
"I don't know the football plan for 20 years inside out but it's a document that actually attacks the wrong areas not the ones that need to be improved.
"A second tier and perhaps a third tier is going to bring value to the Australian game. We need to give our promising kids more opportunities not less."