Further details of the injuries could be given when manager Pep Guardiola holds his pre-match press conference on Friday afternoon.
City had already been dealt an injury blow this week when defender Benjamin Mendy was found to have ruptured the anterior cruciate ligament in his right knee.
"I think days off are to be happy", Guardiola told reporters. We can't replace him in the way he plays, the way he goes up and down.
City were beaten home and away by Chelsea, and Guardiola said the 3-1 defeat at the Etihad Stadium in December was a turning point in their season.
"Aguero has had an accident in Amsterdam and he will be back after that".
He said: "I only knew this morning when I woke up".
Guardiola dismissed suggestions that, quite apart from the unfortunate accident, the flight and late night would not have been the best preparation for any player before a big game.
"I have not spoken to him yet". (KaWijKo Media via AP) Aguero suffered a broken rib from the crash.
"It was his day off, I'm not the police", he said. "Always, I am a manager who doesn't like to train every day", Guardiola, who played pro for almost two decades, continued.
The former Barcelona and Bayern Munich boss is keen to see how his revamped squad respond and will not allow Aguero's absence to serve as an excuse.
However, if the 24-year-old is not fit enough to play a major role on Saturday, the Italian manager is able to call on midweek match-winner Batshuayi, who has scored five in his six club showings this term.
Aguero has made a terrific start to the season, scoring seven goals in all competitions, and City are fortunate that they have so much depth in attacking positions.
"But we have other qualities in other players and have to find a balance with them". They have that ability - they are killers when they have one chance - one goal. Chelsea can not afford to fall behind by too many points early on in the season, something that has plagued them over the last ten seasons.
Guardiola confirmed that Kompany has yet to train with City since picking up an injury with Belgium last month.
"Kompany didn't make one training session with us for one month".