Tyrone could be without forwards Tommy McGuigan and Niall Gormley for up to two months following the injuries the pair picked up in recent club games.
McGuigan, who made his debut in the first round match against Fermanagh, broke a bone in a wrist while playing for Ardboe and Gormley suffered a broken jaw in a game for club side Trillick.
Manager Mickey Harte had hoped the pair could play some part in the Ulster championship but it now appears they will miss the entire campaign.
"Tommy McGuigan is going to be out for a couple of months and Niall Gormley the same," said Harte.
Stephen O'Neill is also extremely doubtful for the Clones tie as the Red Hands continue to struggle with an injury jinx that has continued to decimate the squad for more than a year.
"On top of other intermittent injuries which have kept people out for various amounts of times, it's been a bad follow-up to a bad season of injury.
"But we have to live with that and go on. We can't use it as any excuse. We still have a squad of 38 players here and we want to try and get the best 30 on any given day," Harte added.