The FA confirmed receipt of Wigan chairman Whelan's observations on Wednesday night, but refused to make further comment.
Whelan was branded "a racist" by Cardiff owner Vincent Tan over comments about Jewish and Chinese people in the wake of appointing Malky Mackay as the new Wigan manager.
"The FA will now consider Wigan Athletic chairman Dave Whelan's observations in relation to his recent comments, having received them by today's 6pm deadline," read the governing body's statement.
"The FA will make no further comment at this time."
Whelan had warned he would resign as Wigan chairman if the FA punishes him for the controversy over his comments that so incensed Cardiff owner Tan.
The FA has branded the investigation into Whelan's comments "a priority".
In defending appointing former Cardiff boss Mackay, Whelan told The Guardian: "I think Jewish people do chase money more than everybody else."
Mackay has been recruited by Wigan despite remaining under investigation by the FA for allegedly sending racist and anti-semitic texts
Whelan told ITV News he would resign his Wigan post should he be found guilty by the FA following investigation.
"If the FA look into my affairs - and they were to find me guilty, which I hope they don't and I don't see anything like that happening because I'm absolutely anti-racist, always have been, always will be - however, if they have any questions I'm willing to answer it and, should they even suggest I'm guilty I would immediately resign from my position as chairman of Wigan Athletic," he said.
Mackay has also denied being racist.
Malaysian businessman Tan, who sacked Mackay last December, told Sky Sports News: "Can you imagine if Mr Whelan was the head of the FA? Here we have a racist chairman hiring a racist manager
All the fans in Wigan now think it's okay to be racist.
"They follow the leader
So, how will the FA respond to this? I personally hope the FA is not a toothless regulator in this matter.
"What are Jewish and Chinese people thinking of the UK today? Action must be taken because the world is watching."
The FA confirmed its investigation into Whelan in a statement reading: "We are very concerned to read about the comments that have been attributed to Dave Whelan
We take all forms of discrimination seriously.
"As with all such cases, this will be dealt with as a priority
The investigation is already under way and the FA's governance division have written to Mr Whelan
He has three working days to respond."
Source : PA
Source: PA