Mooy helped the 'Terriers' to promotion from the Championship in 2016-7 before being key in them escaping the drop last season, hence his influence will be sorely missed by Huddersfield.
The Asian Cup will take place in the UAE between January 5th and February 1st, and Wagner admits the absence of the 28-year-old will be a severe setback in Huddersfield's bid for Premier League survival.
Ahead of his side's game with Wolves on Sunday, Wagner remarked: "Aaron has been one of our most reliable and consistent players since he arrived at this football club.
"Performance-wise, he's never happy and is always looking to improve so to be without him throughout January is a huge blow.
"It's something we saw coming six months ago and have to deal with. Will we sign a replacement? It's too early to say, but the next six weeks will be crucial in how we deal with the situation."