"We are taking the matter to a civil court to preserve our rights," Al-Koumi told FilGoal.com on Thursday.
Midfielder Fathi has joined Egyptian champions Ahli from English club Sheffield United on a four-year deal for £675,000.
Ismaili could have received 15% of the transfer fee if it exceeded 700,000 but now they are considering other options in order not to pull out of the deal empty-handed.
However, they could face sanctions in case they pursue their legal action as FIFA regulations prohibit any club from going to civil courts to resolve footballing issues.
Meanwhile, Al-Koumi revealed that he is trying to reach a compromise with Ahli officials regarding Hosni Abd-Rabou's case.
FIFA ruled in favor of Strasbourg in the transfer saga and the French side should have the player at their disposal soon.
Strasbourg had already agreed to sell him to Ahli once he returns to France, the decision which irritates Ismaili who are trying to convince the Red Devils not to proceed with the deal.