The Argentine tweaked his hamstring after scoring a penalty in the 3-0 victory over Stoke on New Year's Day and will learn his fate after undergoing medical tests.
The Argentina international bagged his side's third of the afternoon from the penalty spot following strikes from Pablo Zabaleta and Edin Dezko, yet limped from the field just minutes later to be replaced by Carlos Tevez.
The 24-year-old is now set to undergo scans on the injury on Wednesday, with the initial prognosis suggesting a four-week absence.
However, City manager Roberto Mancini will be boosted by the news that Mario Balotelli has recovered from illness and will be available to deputise.
Following the win over the Potters, City assistant manager David Platt confirmed that Aguero is likely to miss this weekend's FA Cup third round tie with Watford.
"It’s bad enough, he won’t play on Saturday," Platt said in the postmatch press conference. "Its difficult to assess an injury like that [and] how long it’s going to be.
"Saturday he’ll be out and my experience would say he’d be doubtful for Arsenal."
Aguero missed a stint earlier in the season through injury, and Platt remained cautious when estimating how long the forward could be sidelined for with this latest setback.
"There's different degrees of hamstring, that’s why you need 48 hours [to assess]. Its not just 'it’s a hamstring and this is how long its going to be', there are different degrees of the tear that are in there," he continued. "It’s far too early, I haven’t got the qualities to scan his legs. There’ll be a lot of swelling in there, a bit of bleeding in there.
"We won’t know for 48 hours how long it’s going to be and how quick it’s going to settle down. Of course it’s a blow, but I think that’s what you run the risk of"