The FA says that Dave Whelan's remarks "were abusive and/or insulting and/or constitute improper conduct and/or bring the game into disrepute."
The governing body says it is an "aggravated breach" of FA rules because it referred to "ethnic origin and/or race and/or nationality."
Whelan made the comments to The Guardian newspaper while defending his decision to hire Malky Mackay as the second-tier club's manager, even though Mackay is under investigation for sending racist and anti-Semitic text messages.
Whelan has apologized and said he will quit his position if found guilty by the FA.
He has until Dec. 5 to respond to the charge.