The 26-year-old Austria international fractured his cheekbone for the second time during Saturday's 1-0 home defeat by Plymouth on his return from a six-month lay-off after knee surgery.
Cooper said: "It's heart-breaking for him. He has worked so hard to come back from his knee operation and just to get him back on the field was a massive bonus.
"He has been champing at the bit for the last few weeks but he has just not been quite right.
"The manager [Gordon Strachan] saw an opportunity to get him back on the field on Saturday and get him back in the team but he is obviously going to be missing for a little while now and it's a real shame for him.
"But he's a strong bloke and he will be back strong."