Villa are searching for a new manager after dismissing Alex McLeish on Monday and Martinez is one of the names to have been linked with the vacant post.
Martinez was a target for Villa last summer before McLeish was appointed and has enhanced his reputation over the past 12 months by keeping the Latics in the Premier League.
The Spaniard has refused to be drawn on speculation connecting him with Villa and Whelan says there has been no approach at this stage.
"We haven't received any notification at all that Aston Villa want to talk to him about this job," Whelan told Sky Sports News.
"I am not aware of any approach coming from Aston Villa or any other club.
"Roberto and I have a complete understanding where we trust each other implicitly.
"If anything comes up Roberto will see me and I will be the first to know.
"We have a working relationship that is very upfront, open and honest."
Whelan has always insisted that he will never stand in Martinez's way if they both feel it is the right time for the 38-year-old to move on.
The chairman did not think Martinez was ready 12 months ago and believes he is still developing as a manager.
"If anybody approaches him, he will tell me because he knows that if I feel the club is right, and he feels the club is right for him, I will let him go and will back him to the hilt," said Whelan.
"Last year I personally did not think that Roberto was ready to step up to the challenge.
"I believe he is still on the learning curve, but he is a very quick learner, and he is going to go to a top club. That is for sure and I will back him when the time comes.
"I would like to keep Roberto, full stop, at Wigan, but that will be impossible because of how he has revolutionised Wigan again this year.
"We have great plans going forward at Wigan, and he is still very much a part of that."
Asked if he thought Martinez would be Wigan manager when the new Premier League season kicks off in August, Whelan concluded: "I would say at this particular time, definitely, yes."