Leicester City, who won the Premier League in the 2015/2016 season, agreed to sign Portuguese international Adrien Silva from Sporting Lisbon for a reported $28.7 million on the final day of the summer transfer window on August 31.
However, the paperwork was submitted to the English Football Association seconds past the midnight deadline.
And under FIFA regulations Silva is not permitted to play until January 1.
"We can confirm that FIFA has been contacted by the FA in connection with the registration of the player Adrien Silva and the club Leicester City," said FIFA in a statement sent to CNN.
"FIFA has replied accordingly providing reference to applicable regulations."
"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 told CNN in a statement.
Meanwhile, Sporting president Bruno de Carvalho told the club's TV station: "I would like people to realize that FIFA has not ruled against the transfer, but against registration.
"The transfer is done, what is at stake is the registration and I hope you can enrol. Adrien was exemplary. Leicester needs the player a lot and I hope they find a solution."
Transfer matching system
Federations like the FA and clubs such as Leicester and Sporting use FIFA's electronic platform -- the International Transfer Matching System (ITMS) -- to conduct international transfers.
According to FIFA's website "each member association and club assigns specific employees that are granted access to ITMS in order to manage international transfers. They are referred to as TMS managers or TMS users.
"The TMS manager or user must be trained, sign a confidentiality agreement and undergo a background check before being granted access to ITMS."
The FA told CNN that it was working with Leicester to try and find a solution.