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The captain of the London team Cesc Fabregas and defender Emmanuel Eboue suffered injuries in Tuesday's Champions League match against Braga.
The Gunners lost 0-2 in Portugal and in the final round they will have to fight for a victory if they want to secure a place in the knockout stages.
Fabregas has problems with his Achilles tendon, while Eboue is struggling with his knee ligaments.
Talking about the Spaniard, who was not fully ready to play, Arsenal manager Arsene Wenger said: "The treatment could take two or three weeks. I took a risk and it cost us dearly. Eboue will be out for a couple of weeks as well."
