"We have decided to relieve him of his duties because his long absence led to Ismaili being stumbled in two successive matches in the CAF Confederation Cup," Al-Koumi told FilGoal.com.
The former Guinea boss flew to France last month to undergo a knee surgery and provided several excuses for the delay of his return.
Assistant coach Fawzi Gamal took the helm during that period, in which Ismaili drew twice against Sudan's Al-Merrikh and Nigerian club Kwara United as their hopes of reaching the Confederation Cup semis faded.
Al-Koumi revealed that Ismaili have appointed former ENPPI coach Taha Basri as the club's new manager.
"Basri will pen a two-year contract and will earn EGP 45,000 as a monthly salary," he added.
The Egyptian has been out of work since resigning from his post as Arab Contractors coach last April.