The Latics chief has admitted that keeping hold of players of such calibre is difficult as the Reds continue to be linked with a £10 million swoop for the Ireland international
Goal.com exclusively revealed last week that the sought-after 20-year-old was on the verge of a £10 million move to Anfield, with Kenny Dalglish said to be a huge admirer.
The admission of the Wigan chairman will do little to prevent further rumours of an exit for McCarthy, who has also been linked with moves to Arsenal and Chelsea.
Whelan said: “James is a quality young player and the intention is to be keeping hold of players of that calibre.
“In the end, of course, you have to let them go, there’s no question about that. It’s how long you can keep there here and it also depends on what the lad himself wants to do.”
McCarthy played a key role in Wigan’s survival run-in, playing in their last 15 games of the season and scoring two goals to help the Latics overcome relegation rivals Blackburn in February.
He also made his competitive debut for the Republic of Ireland in March after making his first appearance for his country last year against Brazil.