He dismisses the cynics who say he is indebted to his Spanish coach, after Martinez rejected the chance to take charge of Aston Villa last summer.
"I've sacked a few managers here and I had a run where I sacked two within six months or so," Whelan told the Sunday Mirror.
"Everything comes down to what's in the best interests of the football club. Personalities don't come into it.
"What you want is the club being run properly from top to bottom, and Roberto does that.
"Our confidence is in him and if there's any man who could bring our club back up that league, it's Roberto.
"If I thought for one moment that by sacking him I could keep Wigan in the Premier League, I'd do it tomorrow, without question, because I only want what's best for Wigan.
"But I know that would be the wrong thing to do."