The Austrian winger, who joined the Tigers on a two-year deal in September, broke a bone in his foot playing for the under-23s earlier this week and will now be sidelined for a spell.
Mayer has struggled for opportunities of late and has not featured in the league since January 2 and the news represents another blow.
McCann, whose side moved to the League One summit with a fine 3-1 victory at Peterborough on Tuesday, said: “Tommy limped out of the under-23s game, which is disappointing news for us as he is going to miss the rest of the season. He has broken his metatarsal. It is disappointing for Tommy because of the form of Mallik (Wilks), Gavin (Whyte) and Keane (Lewis-Potter) and Dan Crowley coming in and James Scott coming in, he has just found time limited in the first team.
“I have spoken to him and we will pick him up.”
McCann confirmed that Josh Magennis missed the game at Peterborough as a precaution and he and Lewie Coyle will be monitored ahead of Saturday’s home game with Oxford United where City will be chasing a fifth win on the spin.
The latest success at London Road was arguably one of the club’s best results of the season as they registered their tenth away triumph this term.
The game turned just before the break at 1-1 when home midfielder Ethan Hamilton was dismissed for a lunge on Coyle with McCann thankful that the challenge did not result in a serious injury for his player.
McCann added: “I was right in front of it and Lewie was lucky not have his leg broken.
"He had his leg strapped up and we are just hoping he will be okay for the weekend.
“To go a goal behind and come back and win, I am really proud of the side.
"We have shown how quickly the season can spin and turn and there will be a lot more twists and turns. Although people might think I am a broken record, there's 11 games left and the games are coming thick and fast and now we have another tough games against one of the best teams in the division on Saturday in footballing ability and we need to try and pick up the three points.
"But we will not be flustered and will be calm and composed and go out to try and enjoy the game."
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