The 29-year-old sustained an injury in his Turkish club, Sivasspor 2-1 defeat at Ankaragucu on Sunday night.
Musa was treated on the pitch for what looked like a shoulder injury but was later replaced by Cameroon international, Clinton N’Jie on 19 minutes.
A scan will be carried out today to determine the extent of the injury.
Super Eagles head coach, Ahmed Musa has had to rejig his squad following injuries to Leon Balogun and Henry Onyekuru.
The duo have been replaced by Valentine Ozornwafor and Emmanuel Dennis.
The friendly against Algeria is billed for the Miloud Hadefi Stadium, Oran on Tuesday, September 27.