Comments attributed to the Spaniard appeared in a newspaper in his homeland in which he suggested that the Football Association were afraid to punish the Red Devils boss.
Martinez was also reported to have claimed that Ferguson had other Premier League managers - including Sam Allardyce and Steve Bruce - on his side in his battles with Liverpool boss Rafa Benitez.
But the Wigan boss insists he never made any comments about Ferguson and released a statement through the League Managers' Association.
Categorically deniedThe 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."
Ferguson found himself in hot water with the FA over his criticism of referee Alan Wiley's fitness in the wake of the home draw with Sunderland earlier this month.
The Old Trafford supremo has admitted to the charge of improper conduct and has asked for a personal hearing.