Marmoush lasted only a few minutes in the 0-0 draw with Burkina Faso in Tuesday's World Cup qualifier when he went down from a challenge, with the team doctor saying the 26-year-old suffered a bruised knee ligament.
"Initial results on a scan performed in Egypt indicate he will not be available for the Manchester derby on Sunday, and he will now return to Manchester for more assessment and to begin his rehabilitation," City said in a statement.
Marmoush, who joined City in January last season, finished the campaign with eight goals and four assists in all competitions. However, he has yet to open his account this season.
The injury is a major blow for Pep Guardiola's City, who are 13th in the standings after three rounds with just one victory.
City are already without Rayan Cherki and Mateo Kovacic after they suffered long-term injuries, while Phil Foden and Savinho are also doubts.