Fifa has rejected Leicester City's application to register midfielder Adrien Silva after the club missed the deadline by 14 seconds.
The Foxes agreed to sign the midfielder from Sporting Lisbon for £22m near the close of the summer transfer window on 31 August.
Silva's registration was not completed in time with football's governing body meaning the deal was not finalised.
Leicester are in the process of trying to appeal against the decision.
The Football Association has been in touch with Fifa and will look to help Leicester with its case.
A Leicester spokesman said: "We are working with Adrien and Sporting Clube de Portugal to overcome some issues relating to the player's registration and exploring all options to find a resolution."
Leicester still hope to complete the deal but Sporting President Bruno de Carvalho added: "The transfer of Adrien is already completed. Hopefully Leicester find a solution for him."
France-born Silva, 28, is a product of Sporting's academy and has had loan spells at Maccabi Haifa and Academica.
He has earned 20 international caps and played during Portugal's run to winning Euro 2016.
Leicester also sold midfielder Danny Drinkwater to Chelsea for £35m in the final moments of the transfer window.
Analysis - 'A player in limbo'
Registering a player is not just about sending a single file, it's a group of forms which need emailing/faxing/posting over to Fifa by the 23:00 BST transfer deadline.
In this case, Leicester had successfully sent through most of the paperwork on time, bar one form, and because that form arrived late the whole process was rejected. It reminds me of doing my GCSEs and being told that however good my paper was, it would score a zero if I forgot to put my name on.
You have to send a passport, a copy of the contract and several other items before the deal is done. Fourteen seconds might seem like a ludicrous amount of time to squabble over but a deadline is a deadline and if Fifa row back on this now then imagine other clubs saying 'hold on three years ago we missed it by 25 seconds', it would never end.
The only way Fifa could still allow this to happen while standing by their deadline is to ratify Adrien Silva's registration and say that because the documents were on their way (in the post, in the cloud, whatever) that it meets their criteria.
Fifa's statement sounds pretty resolute though, they have listened to the Football Association's case on Leicester's behalf and simply palmed them off by referring them to the regulations.
The player is left a little bit in limbo. The problem could come in that there could now be an argument between Leicester and Sporting. One of the two clubs owns him.
Sporting are saying he is a Leicester player. I get the feeling Leicester might decide if their appeal is rejected that they don't think he's theirs.