The Manchester United defender and his brother, who is on loan at Bursaspor from QPR, were reportedly the subject of a song from visiting supporters saying they should be "burned on a bonfire".
Football Against Racism in Europe (FARE) have contacted FIFA and the Football Association is awaiting official notification regarding the complaint.
The 34-year-old tweeted: "You expect and accept banter from fans on the terraces as its part of what makes the game great, but racism is not banter, and from ya own fans. WOW.
"Always a small minority who ruin it for others.
"Let's not jump to conclusions + assume though as it might just have been banter. We'll see after the investigation."
It is thought Ferdinand may have been targeted by some England fans angered by his decision to withdraw from Roy Hodgson's squad for the World Cup double-header against San Marino and Montenegro.
Ferdinand declined the opportunity of a first cap since June 2011 in order to follow a pre-planned fitness routine designed to help him manage his long-standing back problems.
The 34-year-old drew criticism from some fans when he then flew out to Doha to appear as a TV pundit for the San Marino match.
If FIFA decide that the chants were racist in nature, England could be forced to play a World Cup qualifier behind closed doors.
Last week, football's world governing body forced Bulgaria to play Malta behind closed doors after finding their fans guilty of racist chants during October's World Cup qualifier against Denmark.
And in January, Hungary were fined £27,800 and made to play a World Cup qualifying match against Romania in an empty stadium after FARE lodged a complaint over anti-Semitic chants by their fans during a match with Israel last August.
FARE's executive director Piara Powar said on Thursday: "Although we did not have observers at the match we have pulled together evidence sent to us including media comment and have passed that on to FIFA.
"I think that it's one of those things that is very subtle. We would say racism and other forms of discrimination is not always banana throwing and monkey chants. It can be very subtle and the people collating the reports believed it is strong enough to send on to FIFA.
"From the reports we have seen I personally think there was an undercurrent of race there, and other people have thought that it has been imbued with racist overtones.
"Whether FIFA think that is strong enough to take action is another question entirely and we accept that it is certainly an unusual report."