Shiels saw a specialist this week after being carried off on a stretcher during Rangers' 2-1 defeat by Annan on Saturday.
The injury had already forced Shiels out Northern Ireland's squad for their World Cup double header against Russia and Israel and it looks set to put him out of the remainder of his club's Third Division campaign.
McCoist said: "Dean went down to London on Monday and it is not great news with regards his knee.
"Hopefully it does not require an operation. Without speaking to the specialist myself, which I haven't done, I have spoken to the doctor. It would be very surprising if Dean comes back this season.
"Again rather half-full than half-empty, it looks at this stage as if no surgery will be required."