Last night, Ferguson was asking Nike to look again at the design of the new Total 90 Supremacy boot, which Rooney wore for the first time on Saturday in the game against Chelsea that United went on to lose 3-0.
The company, which began a 13-year sponsorship deal with Manchester United in 2000, has said it is not at fault for Rooney's broken metatarsal, which occurred during a fairly innocuous challenge from Chelsea's Paulo Ferreira on Saturday.
The United manager wants Nike to look at the boot, which has an unusual design, to determine whether it was partly responsible for the injury.
Ferguson said: "There was a lot of weight bearing on the part where [Rooney] had fractured his foot and to be honest, I don't know whether any other boot would have made a lot of difference.
"But it is worth looking into and I will be saying to them again, 'do you think the boot could have had anything to do with it'?"
However, Nike has rejected claims that the lightweight fibres used in modern boot technology resulted in a lack of protection for Rooney's foot, adding that the player participated in all of its trials for the Total 90 Supremacy shoe, which weighs just 10.5 ounces, and suffered no adverse affects.
Cedric Collet, boot developer at Nike, said: "Nothing occurred in any of our tests to indicate the player would be at any risk.
"The boot was specifically designed for Wayne and has incorporated three different types of protection for his foot. In some ways I think these injuries are more linked to the speed the game is played now."
The row could not have come at a worse time for Nike as it faces stiff competition from rival Adidas, which will be on its home turf during the World Cup in Germany and seeking to regain ground lost to Nike.
With Nike's new boot, worn by some of the world's footballers, possibly tainted by association with the injury, this could severely damage its World Cup marketing plans.
A Nike spokesperson said: "We do not believe the T90 Supremacy boot was in any way responsible for or linked to Wayne's injury. Both Wayne and Manchester United's medical staff have confirmed they do not believe the boot was linked to Wayne's injury."
While broken metatarsal injuries have dogged England players in recent years, including David Beckham, Steven Gerrard and Gary Neville, Rooney is the only one of those players contracted to Nike.
The news will come as little consolation to England fans and Rooney's sponsors, as his hopes of participating in the World Cup, which begins in Germany on June 9, appear to be fading fast.
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