N'Zogbia has not travelled with the rest of the squad for a pre-season tour of Austria and wants a move away from the DW Stadium.
The former Newcastle player has made no secret of his wish to leave Wigan and Whelan has admitted if a club offers ?10million he will have to accept their bid.
He told Sky Sports News: "(The team) have gone to Austria today but 'Zoggy' hasn't gone. He is a great lad to have around the club. If we do lose him, and we may well do, because he has expressed a desire to move on, we will miss him enormously. But he is a great asset for any football club who wants him.
"I have always said for ?10million he is an absolute snip, if Stewart Downing can change hands for ?20million I don't know what Charles is worth. He is the fastest, most direct wide player in the Premier League and I have always asked for ?10million and hopefully we will get it and he will move on and be happy."
A bid from Aston Villa of less than ?10million was rejected earlier in the week but Whelan admitted it was highly unlikely N'Zogbia would still be at Wigan when the summer transfer window closes.
"He only has 12 months left on his contract," he added. "I would love to keep him, he is a great lad and a fantastic player, but everything being as it is we have to be sensible and if we get a decent offer, and Charles wants to go, as usual I will honour what the player wants and let him go," he said.
"(Villa) are not the sole bidders, there are another couple of clubs who are desperate to sign him. It depends how much they can pay up front, because we have got to re-spend that ?10million this season just to replace Charles."
Whelan took a similar stance over reports linking former Hamilton midfielder James McCarthy with a move away from Wigan.
He said: "He is a fantastic talent, a great lad who trains fantastically well. We are in talks with his agent starting on Monday or Tuesday next week.
"We will lose James eventually and he will go on to one of the top teams in Europe. He has a lot to learn under (Wigan manager) Roberto (Martinez) here and another season or two seasons here under Roberto and you are going to get a great player," he said.
Source: Team Talk