Martinez has rejected an approach from Aston Villa to remain as Wigan manager.
The Spaniard has today turned down the chance to succeed Gerard Houllier at Villa Park in a repayment of loyalty to the Latics.
Martinez, who took charge at the DW Stadium two years ago, has now been offered a pay rise and a new three-year contract by Whelan.
Whelan stood by Martinez when the club flirted with relegation from the Barclays Premier League last season - escaping the drop only on the final day - and the 37-year-old wants to repay that faith.
Martinez: "Over the last two years the chairman has been very supportive to me and loyal, and now I feel I need to be loyal and supportive back to him.
"I haven't finished my job at Wigan Athletic - there is much work still to be done.
"I don't know how long that will take but such is the belief that I have always had that I would only ever decide to move once the club is ready for a new manager."