Mooy has been a central cog in Wagner’s side for the past two and a half years, but the Australian could miss more than five Premier League matches in January as he heads to the United Arab Emirates to help the Socceroos defend the Asian Cup.
The tournament, which is not covered by a FIFA international window, comes at a terrible time for Huddersfield who are battling against relegation.
The west Yorkshire club are second from bottom on the table and have won just once this season.
The Terriers are having trouble scoring goals, with only six scored in 12 matches in the 2018-2019 campaign.
Wagner says his club will have to “manage” the absence in the Middle East of one of his “stand-out” players.
“This is for sure a situation that we have to be prepared for and deal with,” Wagner said.
“It’s something we saw coming six months ago and we have to manage it. Some teams in the past have to deal with losing players to Africa Cup of Nations.
“Now it’s the Asian Cup where teams will lose some players and it looks like we will be one of those teams who will lose a stand-out player.
“Aaron was and he still is one of our stand-out players – one the most reliable and consistent players since he arrived at this football club.
“More or less, he quickly adapted from playing in the Championship to a higher level in the Premier League.
“He’s a player who always likes to work and always has the aim to progress further. He’s never happy performance-wise and always likes to improve.
“It’s a pleasure to have a player like him in your football club and your team. Apart from his individual qualities, he’s a team player as well.”
Mooy has played in 11 of Huddersfield’s 12 Premier League fixtures this season and has racked up more than 90 appearances for the club in the past two years.
Wagner has not decided if he will delve into the transfer market in January to replace the 27-year-old Socceroo in midfield while he is away.
“Will we sign a replacement? I think it’s too early to say and decide what we have to do,” the German said.
“But I think the next six weeks will be crucial in terms of our decision and how we deal with the situation.
“When you sign a player, you’re 100% certain about their physical skills and ability because you know that through your scouting system.
“Our circumstances here are anything but luxurious and it can take two to three months to adapt.
“Does the player have the right character? This is the much more difficult thing to assess, especially signing players for our football club.”