The 17-year-old defender, previously a target for local rivals Manchester United, was signed by the Blues earlier this year.
However, Rennes claim that the Clairefontaine academy graduate had signed a pre-contract agreement with the Ligue 1 outfit.
And if contract did exist, City’s actions could result in a similar punishment to Chelsea, who were banned last week from registering players during the next two transfer windows following their signing of Lens youngster Gael Kakuta in 2007.
"We can confirm that there is a case pending with FIFA's Player Status Department involving Jeremy Helan, Stade Rennais FC and Manchester City," said a FIFA statement.
However, City have since insisted that Helan was negotiating his release from Rennes prior to the Blues registering their interest in signing the starlet, and acted within the laws of the game.
"Manchester City is aware of the ongoing contractual dispute in the French Labour Courts between Jeremy Helan and Stade Rennais," said a statement on the club's official website.
"The dispute between the player and the club pre-dates any interest from Manchester City.
"Manchester City obviously cannot comment on the case until the French Judicial Process has run its course, however, we are comfortable that we have acted within the rules throughout the process and in no way induced any breach of contract by Jeremy Helan."
Earlier, Rennes technical director Pierre Dreossi had demanded the Eastlands outfit be hit with the same sanctions as Chelsea, believing this case to be a more severe breaching of the rules than the Londoners' capture of Kakuta.
"Manchester City must now realise the consequences of their attitude in the Helan case as it is even more illegal than Kakuta," he said in The Independent.
"We have referred this to FIFA. For us it was strange to have no discussion from City and now, in the week after the Fifa declaration on Chelsea, I would hope that it will be the same thing for Manchester City.
"Kakuta signed up for just a possibility of a full contract. For Helan there was definitely one there, under the terms of the pre-contract agreement, because he had played for his country.
"Manchester United said it was not possible to negotiate with us but for City now this is dangerous, though we are not expecting a decision from FIFA for perhaps several years."
