Salah has been managing an issue since hobbling out of Liverpool's win over Leicester City last month, having been on the end of a rugged late challenge from Hamza Choudhury.
The 27-year-old looked to be in pain again in Sunday's mammoth clash with Manchester City.
He was caught by Fernandinho during Liverpool's 3-1 victory, initially staying down before playing on until the 87th minute, and was seen with his foot strapped up at full-time.
Salah joined up with his international team-mates on Monday, but the Egyptian Football Association (EFA) has announced Salah will play no part against Kenya or Comoros.
"Medical tests have confirmed Salah is not ready for Kenya and Comoros," a statement on the EFA's official Twitter page read.
Salah has nine goals in all competitions for Liverpool this season, including five in his past seven outings.
Egypt face Kenya in Alexandria in their first qualifier of the group stage on Thursday before travelling to Moroni four days later.