The 28-year-old suffered a knee injury in the defeat to Arsenal earlier this month that the club’s medical staff insist will take eight weeks to heal.
This was expected to rule Mooy out of any involvement in the Asian Cup, which kicks off on January 5 with the final scheduled to take place on February 1.
However, Socceroos manager Graham Arnold – having already insisted on getting a second opinion on the injury – has still named the Town midfielder in the 23-man squad with a view to him being involved in the latter stages.
Wagner, keen to avoid a club-versus-country row, admits Australia are perfectly within their rights to explore every avenue in terms of getting such an important player fit.
But the Terriers’ chief also hopes Mooy’s future wellbeing will be the overriding priority.
“Our medical department were clear from the images and the tests that he will be out for around eight weeks,” said Wagner.
“Australia have asked for a second opinion, which we absolutely respect. They came over (yesterday) and will make another investigation (today).
“But I expect this to confirm what we already said 10 days earlier. What I must make clear is that we have to together respect and accept that it is not about the Australia Federation, the Asian Cup, Huddersfield Town or the game against Manchester City at the end of January.
“It is all about Aaron Mooy and his long-term career. We will – and he will – rush nothing and he has to make sure everything heals properly. He has our 100 per cent support in that.
“He cannot – and we cannot – afford for him to have further problems with his knee in the future. It is all about his long-term future.”
Before the injury Town were resigned to Mooy missing a large chunk of the campaign.
He was due to fly out to the United Arab Emirates following the Boxing Day visit to Manchester United meaning he would miss the Premier League clashes with Fulham, Cardiff City, Manchester City and, most likely, Everton.
If the Socceroos, holders of the Asian Cup, reached the final then Mooy would also have missed the February 2 trip to Chelsea.
When naming his squad on Thursday, Australia chief Arnold claimed Mooy’s desire to play in the Asian Cup was the driving force behind physiotherapist Phil Coles arriving in England yesterday with a view to providing a second opinion on the injury.
Wagner added: “Aaron is keen to be 100 per cent fit., that his rehabilitation continues as it has so far and that he has no further issues with his knee.
“This is what he said to me. If this means he plays in the Asian Cup, he plays in the Asian Cup. If it means he does not play then he does not play.
“If it means he does not play for us until February then he does not play until February. The most important thing is his recovery.”
Asked if he was concerned that Mooy, who only came out of his leg brace two days ago, being in the squad may lead to him possibly being rushed back even if not fully fit, Wagner replied: “This is something we can discuss once the decision is made.
“At the minute I have a clear answer from my medical department.”
Mooy’s absence, along with that of Danny Williams, out for nine weeks with a knee injury, means Town are likely to make just one change when hosting Southampton tomorrow.
Steve Mounie, available again after serving a three-game ban following his red card at home to Brighton & Hove Albion, is expected to replace Laurent Depoitre up front.
Meanwhile, Wagner has given the broadest hint yet that loan duo Lewis O’Brien and Jack Payne will remain at Bradford City for the rest of the season.
As with most season-long agreements there is a break clause that allows the Terriers to recall either player once the window opens next month. Payne, for instance, was recalled from a loan stay at Oxford United last January to join promotion chasing Blackburn Rovers.
“We are absolutely happy with these loans,” said the Terriers’ chief, “how both of them are fully involved.
“We wish them all the best and that they can continue getting wins like last weekend (against Walsall). We follow them closely, that is our job. Hopefully they can earn some further points for their football club in the future.”
O’Brien has been a revelation since moving to Valley Parade. He shone even when Bradford were struggling and the midfielder is already a leading candidate to be Player of the Year despite arriving at the League One club with no previous experience of senior football.
Wagner added: “Lewis has made the next steps with this loan, playing competitive football in League One at a big League One club. I am happy with the steps he has taken so far.”