The 29-year-old was substituted after just 10 minutes of Aberdeen's 2-1 loss to Ross County at Dingwall on Saturday.
In an interview soon after the game Dons boss Craig Brown thought that Hughes' knock would clear up, but initial assessment from the Dons physics suggests a longer lay-off.
It appears that Hughes has suffered ankle ligament damage and Brown now fears that the former Motherwell player could be out for the rest of 2012.
The news is another setback for the Dons, after losing Ryan Jack until the new year with a fractured foot while on Scotland Under-21 duty, and having Rob Milsom and Rory Fallon suffering continued problems with their long-term injuries.
Brown said: "It's not good news about Stephen."