Wigan chairman was delighted to see his side preserve their Premiership status with a 2-1 win over Sheffield United - but insisted "justice has not been done".
In a relegation decider, it was the Blades who were sent down after starting the day needing just a point to stay up.
But after West Ham - who are still the subject of potential legal action from United, Wigan, Fulham and Charlton for the controversial signings of Javier Mascherano and Carlos Tevez - beat Manchester United and remained in the division, Whelan was sorry to see Neil Warnock's men relegated.
"I don't think justice has been done. I wanted us to win and stay up and I'm happy," he told Sky Sports 3.
"But for West Ham to stay up is not justice.
"It was a great win for them today but for Sheffield United to go down is not fair and justice has not been done.
"But our lads fought to the death today."
Asked if he thought this season's achievement was better than their promotion season, Whelan was unequivocal.
"Yes, you have to say so. Getting up (is good) but staying up like this - for Wigan to do this today is just unbelievable."
But after West Ham - who are still the subject of potential legal action from United, Wigan, Fulham and Charlton for the controversial signings of Javier Mascherano and Carlos Tevez - beat Manchester United and remained in the division, Whelan was sorry to see Neil Warnock's men relegated.
"I don't think justice has been done. I wanted us to win and stay up and I'm happy," he told Sky Sports 3.
"But for West Ham to stay up is not justice.
"It was a great win for them today but for Sheffield United to go down is not fair and justice has not been done.
"But our lads fought to the death today."
Asked if he thought this season's achievement was better than their promotion season, Whelan was unequivocal.
"Yes, you have to say so. Getting up (is good) but staying up like this - for Wigan to do this today is just unbelievable."
Copyright (c) Press Association
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