Spanish publication AS reported on Tuesday that Martinez had commented on Ferguson's FA charge of improper conduct for comments made about Alan Wiley's physical condition - a charge which the United manager has admitted to - by suggesting that the governing body were treating the case too leniently due to the standing the Scot enjoys in the English game.
Martinez reputedly told the Spanish paper: "They (the FA) have just sanctioned Ferguson for saying that referee was not fit enough and the truth is that they're almost apologising to him for punishing him. Any other coach would have been crushed for that."
The report went on to claim that Martinez had labelled Sam Allardyce and Steve Bruce as Ferguson's "group of faithfuls" and that his fellow Spaniard Rafa Benitez had been unfairly treated during his time in England.
But in a statement published on the official website of the League Managers' Association on Wednesday, Martinez strongly denied making the inflammatory comments.
"Wigan Athletic manager, Roberto Martinez, has today [Wednesday] categorically denied making the comments about Sir Alex Ferguson that have been attributed to him in a number of media reports," a statement from the LMA read. " Martinez has referred the matter to the League Managers' Association."