The Argentine is City's all-time top scorer having notched 199 goals in all competitions for the club.
"He has stayed in Manchester, he didn't come," City manager Pep Guardiola told a news conference ahead of training on Tuesday.
"He's been injured for the last two weeks and he still isn't fit," added the Spanish manager, who was unable to say if Aguero will be fit for Saturday's Premier League derby clash with Manchester United at the Etihad Stadium.
Aguero's absence means a likely start for Brazilian Gabriel Jesus in attack.
There was some good news on the injury front for City with left back Fabian Delph, who has been out since February, fit again and in contention for a place in the starting lineup.
(Reporting by Simon Evans; Editing by Toby Davis)
