Nandy was outspoken in her opposition to the appointment of Malky Mackay as Latics manager following the Scot's alleged racist and sexist text messages.
The matter is currently under FA investigation and Nandy wrote a letter to Mr Whelan regarding, what was at the time, the proposed appointment of Mackay.
Speaking about the letter she said: “I wrote to the club last week asking them to take fans’ concerns into account and ensure any appointment was consistent with Wigan Athletic’s values.
“They have assured me that they have done so and I hope this marks the start of a successful next chapter for the club.”
Her comments, however, failed to impress Mr Whelan who told the Wigan Evening Post that Lisa Nandy “doesn’t understand football”.
“I have invited our MP, the lady, I have invited her to any football match she wishes to come to,” he said.
“Come and watch the match, enjoy it, dine with us afterwards. Whether she’ll take it up or not, I don’t know. I hope she will and if she will I’ll introduce her to Malky.
“I think it’s so important that somebody like the MP - she’s not a Wigan girl by the way, she was imported into Wigan from another area, she’s not a Wigan lass, so she doesn’t understand football.
“But we can try and give her some help, she is invited, she is a friend. I’ve only met her once in my life and I’m looking forward to saying hello to her again and I’m sure Malky would say hello to her.
“All her comments I’ve taken on board and I respect them but I have to make the decisions which I think are the best interest of Wigan Athletic and our town of Wigan. That is exactly what I’ve done in appointing Malky.”
The matter has raised quite a lot of attention in the press with Kick it Out expressing their disregard for the decision to appoint Mackay as manager during an ongoing FA investigation.