Flamini was forced off in the first half of Saturday's 4-1 win over Norwich City after suffering a concussion.
Wenger is waiting to find out how serious the problem before finalising his squad for next Tuesday's showdown with Dortmund at the Emirates.
"He had concussion," said Wenger. "He had double vision, so on the advice of the doctor I took him off because I did not want to take any gamble.
"I don't know if he'll be available for Dortmund, it depends now what the doctors will decide.
"Sometimes they are not allowed to play for five days, it depends how big the concussion was."