Latics manager Owen Coyle said today that the Scottish international will have to have hip surgery and that the minimum length of time he would be out is three months.
Coyle is quoted on the club's Twitter feed as saying: "Shaun will be missing for several months to have an operation on his hip.
"The injury stems from the back injury & although he tried to play through it, the right thing to do for both parties is have it seen to.
"It's a massive disappointment but we'll continue getting stronger together as a group."
Coyle was speaking at a press conference ahead of tomorrow's Europa League match against Rubin Kazan.