The club deny the striker's salaries have been delayed.
"Agogo's allegation is no true. Maybe he's talking about the amount of money that has been deducted by the board a while back," insisted club official, Khaled Refaat.
The former Nottingham Forest forward was recently fined by the Cairo club for staying away from several training sessions.
Agogo, 29, has also had to endure a series of controversies and a drought of goals since his sensational switch from England to Egypt last year.
Late in 2008, he was banned as well as fined by the EFA for making obscene gestures at the crowd during a league game.