The Colombian has attracted interest from a number of clubs and has been quoted as saying he could see himself moving elsewhere.
Whelan, however, believes the 26-year-old will put pen to paper on a new deal.
"We’ll be talking to Hugo when he gets back from the Copa America, and as far as I know he’s happy here. We’d like him to stay,” Whelan told the Wigan Evening Post.
“We’ve not had an offer in for Hugo, and I would imagine Roberto (Martinez) will be keen to get something sorted on that one.
“We do not want to be selling him, though – absolutely not.”
The forward joined the Latics from Mexican side Necaxa in 2009 and has gone on to score 22 goals in 89 appearances for the club, including a last day strike against Stoke City which helped Athletic maintain Premier League status.