Trabzonspor striker Waris sustained an injury in the Turkish Super Lig side's 4-1 defeat to Eskisehirspor nine days ago.
Waris has been replaced in the squad by Mahatma Otoo, who plays his football in the Norwegian Tippeligaen for Sogndal.
Leicester City defender Schlupp also misses out because of a knee problem that he sustained in the Premier League club's 2-2 draw with Liverpool on New Year's Day.
The Ghana Football Association revealed in a statement that Schlupp will be sidelined for three weeks.
Forward Kwesi Appiah, on loan at Cambridge United from Crystal Palace, is one of several members of Avram Grant's 23-man squad set to make their first appearance at the tournament.
Baba Rahman, Daniel Amartey, Frank Acheampong and David Accam will all be making their AFCON debuts.
However, there is disappointment for midfielder Ibrahim Moro as well as defenders Samuel Inkoom and Kwabena Adusei, with that trio all missing out after initially being named in Grant's provisional squad for the competition.
Ghana start their AFCON campaign a week on Monday against Group C rivals Senegal in Mongomo.
Strikers: Jordan Ayew (Lorient), Asamoah Gyan (Al Ain), Kwesi Appiah (Crystal Palace), David Accam (Chicago Fire), Mahatma Otoo (Sogndal).