The Pharaohs, who are back in the continental championship for the first time since 2010, were held to a scoreless stalemate at Stade de Port-Gentil on Tuesday.
The seven-time winners currently sit third on the group table, two points below leaders Ghana.
“The pitch was awful, also humidity and temperature badly affected our players’ performance,” Cuper said of their opening day deadlock.
“Plus, now, I have a crisis after [goalkeeper Ahmed] El-Shennawy was injured during the match.
"This leaves me with two injured goalkeepers and only one ready to start.
“We have no option but to win our match against Uganda.
'Even if Ghana defeat Mali, the group will still be complicated till the last round.”
Egypt face Uganda on Saturday, before rounding off their group stage activities against Ghana four days later.
Goalkeeper El-Shennawy has since been completely ruled out of the remainder of tournament.