"The defeat alerted us that nothing is taken for granted in football," Zaher told FilGoal.com.
"The Egyptian national team are in a trouble now, we have to resolve any obstacles facing us."
The African champions slipped to third in Group 12 after suffering a stunning 1-0 loss to Malawi away from home.
Egypt had hoped to claim their third successive win in the qualifiers but the defeat left them in a state of disarray.
Players' Problems
Zaher called on all parties concerned to put an end to the recurring problems surrounding several of Egypt's stars.
"Hosni Abd-Rabou's transfer saga should be ended and goalkeeper Essam Al-Hadari should play without being subjected to constant verbal abuse."
Abd-Rabou, who was voted best player in the 2008 Nations Cup, has yet to learn where he will play next season due to a transfer wrangle between Ismaili and Strasbourg.
Ahli fans chant angry slogans against Al-Hadari whenever he steps onto the pitch after the veteran goalie joined Swiss side Sion without the Red Devils' approval.
Zaher also voiced his concerns over Amr Zaki's transfer saga. Wigan Athletic are interested in the combative striker, but Zamalek are reluctant to allow him to depart.
"I hope Zaki's future will be clarified soon," Zaher concluded.