The 30-year-old was diagnosed with an injury to his right fibula and will undergo further tests.
"I preferred to keep him in the group," Cisse told reporters.
"Sadio Mane is an important player in our squad, it is important to continue to follow his injury, hoping that in two or three weeks there will be progress. But we are really optimistic.
"We will give ourselves all the necessary means to allow Sadio Mane to recover."
The Senegal team doctor, Manuel Afonso, has flown to Munich to assess the extent of Mane’s injury.
Mane's fitness has been a major cause of concern in Senegal, the current African champions, with state president Macky Sall tweeting on Wednesday: "Sadio, heart of a Lion! All my heart is with you!"
Senegal have been drawn in Group A and play the tournament opener against hosts Qatar on November 20, before going on to meet Netherlands and Ecuador.