Sampdoria says they owe £4million after he moved to Old Trafford in January.
The Serie A side has now sent its complaint to the governing body of world football.
In 2017, Sampdoria sold Fernandes to Sporting Lisbon in a £7.5million deal and they claim that owing to the terms of that deal, they should be paid 10 percent of any future profit made on the Portugal midfielder.
In January, Fernandes was sold to United for an initial fee of £47million going up to a potential £67 m.
“The Serie A side, however, has yet to receive what they think is their cut.
“One year after moving the Lisbon, Bruno Fernandes unilaterally rescinded his contract after Sporting players were attacked by their own fans at the club’s training ground.
But he re-signed with Sporting, who think he was duly signed as a free agent a second time, meaning they don’t owe a cut to the Serie A side.