The Congress, which elects the FFA board, has representatives of the country's nine states and territories but currently just one delegate for all 10 clubs in the top-flight A-League and none representing the players.
The clubs say they generate 80 percent of revenues for football in Australia and want at least five seats on the Congress.
The FFA, however, have offered the clubs two additional votes and one for the players on an expanded 13-member Congress, which both the clubs and FIFA have rejected.
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A joint FIFA-Asian Football Confederation delegation arrived in Sydney two days ago to try to broker an agreement but is departing back to Zurich with no such result, the Sydney Morning Herald and Australian Associated Press (AAP) reported, citing sources involved in the discussions.
However, the FFA said discussions were continuing.
FIFA will disband the FFA if no solution is reached by Nov. 30. The global body as said it would install a 'normalisation committee', which would effectively take over governance of the sport.
"We are bitterly disappointed at not having reached consensus with our fellow stakeholders," Greg Griffin, chairman of Adelaide United and of the Australia Professional Football Clubs Association, was quoted as saying by both the AAP and Sydney Morning Herald.
He accused the FFA board of "obstructing the process".
FFA Chairman Steven Lowy said in a statement on the FFA website (www.footballaustralia.com.au) that the federation was still hopeful of an agreement before the deadline.
"A wide range of options has been robustly discussed over the past 48 hours," he said.
"Everyone, including the FFA Board, A-League club owners, Member Federations and the PFA have shown willingness to move from their original positions and this has been noted by the FIFA/AFC delegation."
(Writing by Simon Jennings in Bengaluru; Editing by Raissa Kasolowsky)
