The Socceroos could have secured their sport in Russia 2018 with a comprehensive win against Thailand earlier this month.
Instead they now face a lengthy playoff route.
For Wagner this means Huddersfield will be without Mooy for the duration of the upcoming international window with the star midfielder set to join his Socceroos teammates in Malaysia early next week for their do-or-die World Cup playoffs against Syria on October 5 and Sydney's ANZ Stadium on October 10.
The Premier League new boys could also be without Mooy for two weeks in November if the Socceroos win the tie against Syria.
Australia will take on the fourth-placed finisher from North America in a home and away tie on November 6 and November 14.
Mooy has played a starring role in the Terriers' successful start to their maiden Premier League campaign and coach Wagner could think of nothing worse than losing one of his key players for an extended period.
"What I wished was that they (Australia) had already qualified for the World Cup and he (Mooy) not have to go off again and play Syria and then maybe again for another playoff after that," Wagner said.
"If after the season he has qualified for the World Cup and gets the chance to play in the World Cup I would be very happy for him.
"But I would be much happier if we finish the season with a positive result for the club (without losing him) and the he goes to Russia after the season.
"It is something I have to accept and deal with. There is nothing I can do about it so there is no point spending too much time thinking about what I wish."
After helping the Terriers win promotion following a breakout season in the Championship in 2015-16, Mooy has continued his rapid rise from emerging star to Premier League midfield maestro.
It is something which hasn't been lost on Wagner who was quick to praise the former Melbourne City and Western Sydney Wanderers player.
"Aaron has been quick to adapt to the Premier League and has been very good in all of our matches so far," Wagner said.
"He has been able to score, make assists and control the tempo of games so we are very happy with his performances.
"It is only early in the season so Aaron will need to work hard and improve because in the Premier League it will only get tougher each week."
Mooy will return to Premier League action when Huddersfield host Tottenham Hotspur on Saturday.
*Watch Huddersfield Town v Tottenham Hotspur live, free and in HD on SBS Australia or live stream on The World Game app from 9pm on Saturday September 29.