Whelan was charged with improper conduct and bringing the game into disrepute for comments in made in The Guardian newspaper shortly after Malky Mackay became Wigan’s new manager.
Mackay is under investigation for sending racist and anti-Semitic text messages and Whelan made the comments while attempting to defend his new appointment.
The 78-year-old originally threatened to resign as chairman of the Latics if found guilty of racism by English football’s governing body but now seems to have changed his stance.
Although he accepts the charge and apologised for the comments, Whelan maintains he was misquoted and misrepresented in the interview.
After charging Whelan, the FA said in a statement: "It is alleged the Wigan Athletic chairman breached FA Rule E3 in that his comments were abusive and/or insulting and/or constitute improper conduct and/or bring the game into disrepute.
"It is further alleged that this is an 'Aggravated Breach' as defined by FA Rule E3 as it included a reference to ethnic origin and/or race and/or nationality and/or religion or belief."