Wigan's appointment of Malky Mackay as manager attracted criticism this week, after the Scot was reported to the FA over his exchange of text messages with Iain Moody - former head of recruitment at Mackay's old club Cardiff City.
Mackay admitted the messages were "disrespectful of other cultures" and he has come under investigation from the FA.
Whelan was then forced to apologise for comments he made in an interview with The Guardian, where he suggested there was not "a lot wrong" with anything Mackay had said in those messages.
And the 77-year-old provoked widespread outrage when he described Jewish people as "chasing money more than everybody else".
Kick It Out called for the governing body to look into the matter and on Friday, the FA confirmed that it would contact Whelan over the matter.
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