The midfielder will miss the World Cup qualifier against Austria after picking up a hamstring injury in Friday's 2-1 loss to Sweden in Dublin
Giovanni Trapattoni's plans ahead of the crucial fixture have been disrupted by the news that a hamstring problem will sideline midfielder Whelan, who has withdrawn from the squad. Hull City's Stephen Quinn has been drafted in as a replacement.
Stoke City stalwart Whelan played the full 90 minutes in Friday's 2-1 defeat against Sweden, a result that left Ireland fourth in Group C, three points adrift of second place.
Ireland head to third-place Austria searching for a win to keep their World Cup hopes alive, while they will also hope Kazakhstan can do them a favour at home against Sweden.
Whelan has won 50 caps for his country, reaching the milestone on Friday.
But the occasion was not a joyous one, as goals from Johan Elmander and Anders Svensson gave the Swedes victory in Dublin.