The Spaniard, who kept the club in the Barclays Premier League thanks to a four-game unbeaten run at the end of the season, has spoken to Villa officials who are looking for a successor to Gerard Houllier, who stood down earlier this month for health reasons. Whelan confirmed Villa had approached him but expects the 37-year-old to remain at Wigan.
He said: "Aston Villa have acted above board and in a totally professional manner. They wrote to me asking for permission to speak to Roberto. He was on holiday at the time and I granted Villa permission. He arrived back yesterday and I presume he has spoken to Villa. I have made it clear to him I will be extending his contract."
Whelan added: "I have never let him down on anything and he has never let me down. I know I can never say never in football, but I would be very surprised if he is Aston Villa's new manager."
Bolton boss Owen Coyle has also been linked with the Villa vacancy, while the prospects of two other men linked to the job - Steve McClaren and Rafael Benitez - appear to have receded.
It has been reported that Villa opted against even interviewing McClaren after fans reacted negatively to the prospect of his appointment based on his poor record as England manager, while former Liverpool boss Benitez is reported to have asked for Villa to commit to a transfer budget.
Villa were understood to be interested in speaking to former Chelsea boss Carlo Ancelotti immediately after Houllier's departure was confirmed, but the Italian has now stated he wants to take a year out of the game, while Mark Hughes does not appear to be in the frame despite being available following his resignation from Fulham.
Source: PA
Source: PA