A brilliant start to the Premier League season saw Mooy cement himself in Huddersfield's starting 11, but the 27-year-old has failed to complete a full 90-minutes in his side's last three outings.
“Even I have seen he looked tired in the last two games,” Wagner said.
“I have seen it, and we have managed him individually in this week in training as well.
“We have to make the right decisions in the next games ... to make sure we get him back to his best freshness, mentally first and foremost, and physically as well because he is a very important player for us, as everybody knows.”
Mooy was dropped against Manchester United on Sunday (AEDT), with goals to Romelu Lukaku and new signing Alexis Sanchez helping Jose Mourinho's men to a comfortable 2-0 win.
“I’ve had conversations with him, of course, like I have conversations with all of my players," Wagner said.
“We have spoken about it and he is very self-critical. He knows that he wasn’t on his best.
“He knows, as I do, that we have to get him every support and every help to come back to his best.
“There are no arguments between him and me about his performances, over the whole season, too, obviously.
“We all together should not forget he has been very strong and a big performer for us as well.”
Mooy has played 26 Premier League games this season - scoring four goals along with two assists - for the Terriers, who are now languishing in the relegation zone.