The England winger sustained the injury during Arsenal's 5-2 derby win over Tottenham at the weekend but was able to play on and scored the Gunners' fifth goal in injury-time at the end of the match.
Arsenal boss Arsene Wenger revealed Walcott had not trained today (Tuesday) and would have a scan to determine the extent of the injury although he thought it would be only a short-term thing.
Left-back Kieran Gibbs and Ivory Coast midfielder Gervinho are back in the squad for the Emirates Stadium tie but Andre Santos is out injured with a stomach problem.
Wenger said: "Walcott is an important part of what we want to achieve this season. We started the season with this squad, and we want to finish the season with this squad.
"We want to win because we have a good opportunity to finish the job and qualify."
Montpellier's Senegal striker Souleymane Camara is suspended for the north London encounter having received his third yellow card of the group stages in the defeat to Olympiakos.
Morocco forward Karim Ait-Fana is a long-term absentee after injuring his right knee in training last month.