In a cruel blow to the Socceroos' 2019 AFC Asian Cup chances, Mooy was ruled out for seven weeks by the medical team at his Premier League club, who diagnosed him with a tear to his medial collateral ligament in his right knee.
Despite the advice from Huddersfield's doctors, the FFA are still holding out hope of Mooy playing a role in the the tournament which will be held in the UAE next month.
Australian officials have pledged to leave "no stone unturned" in a bid to get Mooy healthy, and have sent their own doctors to provide a second opinion on the severity of the injury.
Wagner said he was not concerned with the FFA's decision and said his Premier League side has kept 'no secrets' about the Aussie midfielder's injury.
"I totally understand and we will support them if they like to have a second opinion, that’s their right," Wagner said.
"We would love to have him back earlier, but everything my medical department said is that he will be out for eight weeks unfortunately. This means for them he misses more or less the whole Asia Cup.
"If they want to bring some medical staff over to have a look at Aaron, they can. We have already given them our images from his scans and the reports from the specialist as well. We have no secrets about it.
"It’s anything but nice for all of us."
