Two votes for Mohamed Salah in the Best Fifa men's player award were not counted because signatures were in capital letters, says Fifa.
The Egyptian Football Association (EFA) said acting Egypt coach Shawky Gharib and captain Ahmed Elmohamady voted for Liverpool forward Salah.
Fifa said: "The signatures on the voting forms were in capital letters and thus seemed not valid."
The forms also lacked a mandatory signature by the EFA general secretary.
Barcelona's Lionel Messi won the award on Monday ahead of Juventus forward Cristiano Ronaldo and Liverpool defender Virgil van Dijk.
Salah finished fourth in the voting, although the invalid votes would not have affected the standings.
Football's world governing body Fifa said voting was supervised and monitored by independent observer PricewaterhouseCoopers (PwC) Switzerland.
It said it contacted the EFA twice on 19 August to submit properly signed voting forms but did not receive a response in time for the votes to be counted.
Fifa also said the Egyptian FA had "undergone a few structural changes" after the voting period opened.
Since the awards ceremony Salah has removed "Egypt" from his Twitter profile, which now reads: "Footballer for Liverpool FC."
He also posted a tweet which translates as: "Whatever they do to try to change my love for Egypt, they will not succeed."
Egyptian Football Association president Amr El-Ganainy said he talked with Salah. He said: "I talked with Salah explained to him it was an administrative mistake."
In 2018, Salah came third in the men's award and also took the Puskas award for goal of the season.
Each nation has three voters - the national team coach, the national team captain and a media representative - who each select their top three players in the world.
The EFA said Gharib and Elmohamady picked Salah as their first choice.
The media representative Hany Danial's choices were Sadio Mane followed by Cristiano Ronaldo and Salah.
Salah threatened to quit the national team last year following a row over his image rights.
More voting controversy...
Nicaragua captain Juan Barrera called into question the authenticity of his country's votes in the awards as he said he did not submit any votes.
Fifa's records show that Barrera voted for Lionel Messi as best player and Liverpool's Jurgen Klopp as best manager.
"I did not vote in the awards #TheBest2019 any information about my vote is false," 30-year-old midfielder Barrera tweeted.
Fifa said it has asked the Nicaraguan Football Federation to investigate the matter after receiving "votes signed by the player".
The Nicaraguan federation have been approached for comment.
The Sudanese Football Federation also said its published votes did not match the votes it cast.
Fifa said: "We have checked the voting documents submitted by the Sudanese FA and all documents are signed and confirmed with the official stamp of the Sudanese FA.
"Having compared with the vote sheets, we confirm that we have the right votes signed by the player/coach. We are asking the Sudanese Football Federation to inquire on this matter."