The 28-year-old suffered the suspected medial collateral ligament (MCL) injury against Arsenal earlier this month and after being assessed by Town doctors, the club announced the Australian playmaker would be out until February - an absence that would see him miss the green and gold's title defence in the UAE through the month of January.
But the FFA have refused to back the judgment call on the injury by the Premier League club, and have organised an independent assessment of Mooy's knee on December 21 with Socceroo senior physiotherapist Phil Coles attending.
National team coach Graham Arnold was diplomatic in a statement released by the FFA, stressing that Australia was doing their due diligence on Mooy because of the Asian Cup's importance, but the player's long-term concerns were always number one.
"We have agreed on this plan with Huddersfield Town and know that they are doing everything they can to manage Aaron’s injury," Arnold said.
"However with such an important tournament coming up for Australia we want to explore every option available to give Aaron the chance to feature for the Socceroos in the United Arab Emirates.
"Of course, Aaron’s long-term career and fitness remains our primary concern and we will not rush him to return to match play before he is safe and confident to do so, however we are also committed to leaving no stone unturned in our attempt to have him available for us at the tournament."
The loss of Mooy, arguably Huddersfield's best player, through December and January represents a huge blow to David Wagner's team, who are currently two points shy of safety in the Premier League's relegation zone.
Australia's Asian Cup campaign begins with a match against Jordan in Abu Dhabi on January 6 (AEDT) as the tournament builds up to its final match on February 1.