Ferdinand, whose brother Anton was the subject of racist abuse from Chelsea captain John Terry last year, did not wear a campaign t-shirt in the warm-up to United's Premier League match against Stoke despite Ferguson saying on Friday that all his players would. Ferguson described the incident as "embarrassing" and promised to "deal with it".
But Professional Footballers Association chairman Clarke Carlisle told BBC Radio 5 Live: "We will definitely monitor the situation very closely and make sure Rio Ferdinand's rights as a human being, never mind as a footballer, are not undermined in this position."
He added: "Everyone has a right to free speech - just like you can't coerce anyone into shaking hands, you can't make somebody wear a T-shirt - although I do personally believe that joining in with the campaign is the best way forward.
"And then for all these players to get together and put what it is they want down on paper so we together as a union - all the players, one with another - can make those changes and move forward."
The former Burnley player believes communication is key and urged Ferguson to follow the examples of Reading boss Brian McDermott and Newcastle manager Alan Pardew in allowing Ferdinand to explain the reasons behind his decision.
It was the declaration of Reading striker Jason Roberts on Thursday that he would not be wearing a Kick It Out shirt after becoming frustrated by what he perceived as the group's lack of action over racism that earned a rebuke from Ferguson.
Carlisle added: "There are two sides to this one.
"First of all, Sir Alex Ferguson is continual in his unwavering support for the Kick It Out campaign which is commendable and what we all want to see but you can't vilify or coerce any individual for making a stand.
"This shouldn't be seen as an element of control or defiance - just like Sir Alex Ferguson said when he was talking about Jason Roberts in his first interview, he doesn't know the reasons why this stand is being made and what we should do first of all is hear those reasons and listen to them and take them on board."