Aguero is set to miss City's vital Champions League match away to Roma this Wednesday. The striker suffered a knee ligament injury in the early stages of saturday's win over Everton at Eastlands. The Argentinian has scored 19 goals so far this season.
Pellegrini told the Manchester Evening News;"He has a problem in his ligament, in his knee. We will see how serious it is but it's not good news, I don't think he will be able to play next week.
"We must wait for the doctor but the important thing is he will not be playing against Roma and it's a very important game for us.
"But we have other players and we will rearrange if he does not play."
To progress in this season's Champions League City need to win and hope CSKA do not beat Bayern, or get a score draw and hope CSKA lose.
City are already missing Yaya Toure through suspension, and Vincent Kompany and David Silva arestill battling to prove their fitness.