The Argentina international missed Saturday's 3-1 win over Bournemouth and is doubtful to face Watford and Chelsea this week.
"The doctors told me (on Friday) Sergio cannot play," Guardiola said. "If he plays, maybe it's four or five weeks off. In that situation, this month, with a lot of games, he was not safe."
City's all-time top scorer appears unlikely to make the trip to Vicarage Road on Tuesday or Stamford Bridge on Saturday.
"Right now, I'm not quite sure," Guardiola said when asked about the availability of Aguero, who has eight Premier League goals this season.
"I speak with the doctors every day, they make a report and a briefing," he added. "They say 'ready' or 'not ready' and we decide."
Gabriel Jesus started against Bournemouth in Aguero's absence but was unable to add to his single league goal so far this season for the Premier League pacesetters.
Aguero's form has limited the Brazilian's playing time recently but the 21-year-old said he was ready to contribute if needed following his own injury concerns, which saw him miss last week's Champions League win over Lyon.
"I've been training really hard, maybe that's why I felt something in my groin last week," Jesus said. "Unfortunately I was out of the Champions League match that I really wanted to play.
"I always make it clear for Pep that I'm here to help the team regardless of how. Obviously that I want to play more minutes, but I respect who is playing at the moment."
Guardiola praised Jesus's all-round contribution against Bournemouth and said he had no concerns over the lack of league goals.
"We just relax," Guardiola said. "It's work, this work ethic he has. Always I said to him -- when you work like he works on the pitch, always we will sustain him. We will always be there."
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