The 28-year-old was brought in by Leicester just before last week's transfer deadline to replace midfielder Danny Drinkwater who had been sold to Chelsea.
But media reports said the paperwork was filed to world governing body FIFA, who handle international transfers, moments after the deadline for registration closed.
Asked to confirm if FIFA had rejected the paperwork sent by Leicester and refused to sanction the deal, a FIFA spokesperson said: "We can confirm that FIFA has been contacted by The Football Association in connection with the registration of the player Adrien Silva and the club FC Leicester City.
"FIFA has replied accordingly providing reference to applicable regulations," added the spokesperson.
The FA did not immediately respond to a request for comment on the situation.
A Leicester City spokesman told the BBC: "We are working with Adrien and Sporting to overcome some issues relating to the player's registration and exploring all options to find a resolution.