Agogo moved to the Egyptian Club from English Championship side Nottingham Forest after helping the Black Stars win bronze at the 2008 Africa Cup of Nations.
The player who signed a three-year deal worth £750,000 had his deal abrogated just nine months into his contract forcing the ex-Ghana international to report the issue to the Court of Arbitration for Sports who eventually ordered the North Africa Club to pay the arrears.
FIFA on Wednesday served a notice to Zamalek to pay the remaining arrears of $450,000 or face sanctioning from the World Football governing body.
Junior Agogo until recently battled a stroke after retiring from active football back in 2012.
Zamalek is likely to face a huge penalty should they fail to meet a deadline set by FIFA.