The Potters said the Italian FA told them Shaqiri has a one game suspension over his sending off last season in the Coppa Italia.
The club expressed their disappointment over the decision and said in a statement: “Unfortunately, the clearance from the Italian FA carried a sporting sanction of a one-game ban which applied to the Coppa Italia competition last season.
“In accordance with FIFA regulations, the FA have no alternative but to implement the suspension of another association, but the club have expressed its disappointment that the suspension has been applied to a Premier league fixture this season rather than to a competitive cup competition fixture.”
Shaqiri, who has 46 international caps, agreed a five-year contract to become the Potters’ ninth summer signing.
He could now make his debut for Mark Hughes’ side against Norwich City next Saturday.