The Liverpool talisman was regarded as one of the frontrunners for the award with Barcelona's Lionel Messi and team-mate Virgil Van Dijk.
Salah scored 27 goals and provided 13 assists last season, as the Reds conquered Europe for a sixth time.
The African player of the year for 2018 was in the hunt for his biggest individual accolade to date.
Messi walked away with the award once again – but FIFA have come under some scrutiny for Argentine's win.
Some players claimed that they didn't plump for Messi, but votes were counted towards the Barça ace anyway.
And now FIFA has admitted that some votes for Salah weren't counted at all.
According to Sky Sports, FIFA would not accept the votes of Salah's compatriots Shawky Gharib and Ahmed Elmohamady because of capitalised signatures.
Because the names were written in block capitals, officials couldn't be sure that they weren't fraudulant and thus dismissed them.
FIFA commented that the signatures "were in capital letters and thus seemed not valid (not authentic)", and that "voting forms were also not signed by the [federation] general secretary which is mandatory".
Football's governing body insists that they sent the Egyptian FA "two reminders to submit the properly signed voting forms on August 19".
Salah was initially upset by the seeming lack of support from his fellow countrymen and even removed 'Egypt' from his Twitter bio.
He also posted a tweet which translated: "Whatever they do to try to change my love for Egypt, they will not succeed."
However, he may be reconsidering somewhat after FIFA revealed it was not a matter of disloyalty, but rather red tape.
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