FFA are at loggerheads with their professional clubs over the governance of the game in Australia, with world governing body FIFA stepping in last year in an attempt to end the long-running power struggle.
Elections for the board are in November with nominations due by Sept. 30.
"The main purpose is to give the game every possible chance over the next couple of months to expand the (FFA) congress and at the same time preserve the independence of the FFA board," Lowy told reporters in Sydney.
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"By removing myself from the debate I hope to encourage a proper analysis of the real issues so that an outcome can be achieved that is in the interests of the whole of the game."
The FFA and the professional A-League clubs are locked in a battle over the reform of the federation's congress, which elects members to the executive board.
The congress has representatives of the country's nine states and territories but just one delegate for all 10 clubs in the top-flight A-League, and none representing the players.
The clubs, who say they generate 80 percent of the sport's revenues in Australia, want at least five seats but the FFA offered only four.
"So much of the debate about this struggle over governance has been ... superficial and simplistic," Lowy added. "This has obscured the core principle ... we shouldn't allow representation to be delivered by money.
"We are now at a tipping point: the game either gets stronger or it could break if vested interest prevails.
"The game has so much momentum ... but this could be seriously at risk in a short space of time."
(Reporting by Greg Stutchbury; Editing by Peter Rutherford)
