The 23-year-old had hoped to recover from an injury sustained in Premier League action in time to face Chile and Venezuela but has declared himself 'almost ruled out'
The 23-year-old was substituted in the 4-0 victory over Blackburn Rovers at Ewood Park last weekend after suffering from a groin problem.
Aguero had declared via his Twitter account that he was to meet up with the national team squad on Monday, but has been told he is very unlikely to take any part in the upcoming games.
"I am almost ruled out," Aguero said, according to EFE. "The doctors say this is a very tricky injury.
"I am sorry that this is happening in this good moment I am going through at Manchester City, I was hopeful of at least getting to play the Venezuela match, but the doctors have told me they will not take risks."
Aguero has been in fine form since his arrival at Manchester City, scoring eight Premier League goals.
It is unclear whether the striker will be available for the Blues' clash with Aston Villa on October 15, or the Champions League tie with Villarreal three days later.