The clubs were officially charged with bringing the game into disrepute by way of the misconduct of their supporters on Saturday 28 December in Melbourne.
And the FFA told the clubs that their public statements this week on the events of 28 December are regarded as inappropriate and damaging to the interests of the Hyundai A-League.
FFA has given each club until 5pm next Tuesday to show cause why they should not face sanctions for the alleged breaches.
FFA has warned the clubs that the proposed sanction is the deduction of three competition points from each.
The sanction would be suspended until the conclusion of the 2013/14 season, subject to the proper conduct of supporters for that period.
If the sanction were to be triggered by further misconduct, the three points deduction would apply in addition to any other sanction that may be imposed at that time. 
FFA CEO David Gallop said today that deduction of competition points would be an unprecedented step for the Hyundai A-League.
“The loss of points that have been won fairly on the pitch is a harsh penalty, but it’s in equal measure to the enormous damage caused by the type of anti-social behaviour seen in Melbourne last Saturday,” said Gallop.
“The troublemakers are hurting the club they claim to support. They need to understand that the consequences of their reckless conduct will be felt on the A-League competition table if trouble persists.”
Gallop said that true fans would never dream of damaging their club’s best interests.
“I have great sympathy for the overwhelming majority of fans who like me are sickened by the misconduct of a few, but it’s time to make the consequences clear to everyone,” he said.
“We want a safe, enjoyable and family-friendly environment in the A-League. That’s why we are taking this action. We are absolutely determined to rid the game of the type of behaviour was saw in Melbourne last Saturday.”
The disciplinary action undertaken by FFA is based on extensive briefings and detailed reports on the 28 December incidents from Victoria Police, stadium managers and FFA’s security advisers.