Martinez is top of Everton's list to replace Manchester United-bound David Moyes, as exclusively revealed by Goal.com.
However, Whelan insists there are bigger clubs interested in Martinez and, though he hopes the manager will stay, the Latics owner will accept any decision he is given by the 39-year-old.
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"He has had numerous offers. There are clubs bigger than Everton looking at Roberto every season because he's a quality manager.
"We have a partnership, we have complete trust in each other, that's how we operate. Of course, we would love him to stay but what he decides I will accept.
"The first season [after relegation] is the one to get back up - the parachute payment is the biggest and we should have the same core of players."
Whelan accepts that Wigan were "not quite good enough" to stay up this season, but says it has still been a fantastic season and all he rues is that luck was not on their side.
"The FA Cup is monumental and historic but to be in the Premier League is so important commercially and financially," Whelan added.
"What made the difference this season is that Lady Luck deserted us. We had the most horrendous luck with injuries - sometimes eight first-choice players out with injury.
"We accept that overall we were not quite good enough but we also feel hard-done by. The writing was on the wall when we lost to Swansea at home.
"It has been a fantastic season and I do think Wigan Athletic have made an awful lot of friends worldwide - not judt in the Premier League - because of the way we play and our attitude."