Shakhtar Donetsk claim they are still owed £475,000 as part of the deal that saw Elano join Manchester City last summer.
The Brazilian playmaker moved to Eastlands at the beginning of last season in a deal worth £9.5million for the Ukraine champions.
Donetsk believe City still need a pay a 'solidarity payment', which usually equates to five per cent of the total sum of the deal.
The payment is distributed between clubs that played a part in the youth development of the player, however, City reportedly think the selling club are responsible for the payment.
Fifa have now confirmed they have received a complaint from Donetsk and that they will unveil their findings in due course.
"We can confirm Donetsk have lodged a claim with Fifa regarding this matter," said a Fifa spokesman.
"As the relevant procedure will start in due course, we can't provide further comments for the time being."