The blunder meant the choices of Southampton midfielder Steven Davis and Michael O'Neill were not counted.
The pair were the only Uefa representatives not to have a say in the contest to decide the world's best player.
"The original documents were not received on time," the IFA admitted.
Davis's top three were Portugal captain Cristiano Ronaldo, 30, Argentina forward Lionel Messi, 27, and Dutch winger Arjen Robben, 30, with O'Neill also going for Ronaldo in first place, followed by German World Cup winners Philipp Lahm, 31 and Thomas Muller, 25.
Fifa confirmed that it sent out a reminder email before the closure of the ballot.
A Ballon d'Or spokesman confirmed: "The online votes were recorded before the deadline; however the original documents with the signatures were not received on time. We need to have it, because only than the votes are valid."
One hundred and eighty one national football associations voted in the global poll, while 27 countries did not return any nominations.
Journalist Jackie Fullerton, who voted for Ronaldo ahead of Bayern Munich's Muller and Barcelona's Messi, was the sole Northern Irish representative.
Real Madrid forward Ronaldo won the Ballon d'Or, his third title, with 37.66% of all votes.
Northern Ireland's captain and coach did not get a vote in the Ballon d'Or poll, as the Irish Football Association (IFA) did not send the ballots on time.