The Spaniard was quoted in the Spanish press that he believed the Football Association were afraid to punish Ferguson.
He told Spanish newspaper AS: “Ferguson has his group of loyalists among other coaches – Steve Bruce, his ex-player, and Sam Allardyce, who thinks he will be his successor, among others.
“On the other hand, there is only Benitez and they throw sticks at him from all sides.”
“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,” Martinez added.
“Any other coach would have been crushed for that.
“Ferguson has been here for a lifetime and that carries a lot of weight.”
Martinez has in a statement denied that he has made the comments.
The statement read: “Wigan Athletic manager, Roberto Martinez, has today categorically denied making the comments about Sir Alex Ferguson that have been attributed to him in a number of media reports.
“Martinez has referred the matter to the League Managers Association.”