Hamilton has just two races and effectively six more days on track with McLaren before he brings his 14-year association with the team to an end in Brazil next weekend.
In seeking a new challenge in his career, Hamilton last month signed a £45million, three-year contract with Mercedes, a team that has won just one race since their return to Formula One in 2010.
Whitmarsh was unequivocal in his comments, claiming he was still at a loss as to the reasoning behind Hamilton's decision, one he respects, but which he also concedes he remains "disappointed" by.
And when asked whether he felt Hamilton was regretting his decision, Whitmarsh replied: "I think he has on occasions, yes.
"I hope he thinks he's made an awful mistake, and I hope he thinks that next year."
Ahead of this weekend's United States Grand Prix that is back on the calendar after a five-year absence. Hamilton has dismissed Whitmarsh's suggestions, instead believing they were borne from emotion.
Asked as to how he felt about the remarks, Hamilton said: "I was a little bit surprised to hear it, but it (regret) is absolutely not the case.
"I've a great team, I've been with them such a long time, and I'm sure everyone has emotions within the team.
"But I'm still here, giving 100 per cent to them for the last two races, and of course it's quite emotional for me.
"But I'm very, very happy with the decision I've made."
The decision may well be one Hamilton regrets in time, especially if Mercedes, fighting to hold on to fifth position in the constructors' championship, are unable to forge their way to the front.
As Hamilton sat behind Fernando Alonso and Sebastian Vettel, he was asked how much he would love to be in their position in fighting to become a three-time world champion, and to express how much respect he has for them at present.
As someone who will depart McLaren with only one title to his name in six years with the team, the question likely hit a raw nerve.
Hamilton drew in a deep breath before giving a diplomatic, considered opinion as he said: "It goes without saying they are two of the best here.
"What they've achieved is incredible, with the rest of us aspiring to try to do the same.
"They're both incredibly professional, and it's amazing to see how focused they are considering how much pressure is on them, but they are both world champions and they're handling it, no problem.
"As for me, it is what it is. I'm happy to be here fighting in the last two races with my team.
"I just want to do the best job and try to still fight with them, even though we are not fighting for championship."
Hamilton should be in a position where he is competing for a second world crown, but two failures in the last five races - in Singapore and Abu Dhabi - that have forced him into retirement when leading have scuppered his hopes.
In between, there have also been niggly reliability issues to leave him 90 points adrift of Vettel, who is 10 points clear of Alonso.
Hamilton naturally has no intention of becoming embroiled in their private battle, but he remains fiercely determined to savour one more win before he leaves McLaren.
"We don't want to get in the way of anyone," said Hamilton.
"But we want to beat them, we're still fighting for position in the championship, even though we're not fighting for the top position.
"Kimi (Raikkonen) did a great job in winning the last race in Abu Dhabi, where we were very strong as well.
"Hopefully we'll have less reliability issues this weekend and we can compete right at the front with these guys."
Raikkonen, who benefited from Hamilton's misfortune by claiming his first win for Lotus, is of the same mind as the Briton when it comes to being involved in the Vettel-versus-Alonso title tussle.
"We will always try to do the best we can in the race," said the Finn.
"Should we end up taking some points away from either of them, that's racing, that's life.
"But we won't be trying to disturb anything. We'll just try to have a normal race and we'll see what happens.
"I'll try to win, and if not, I'll try to score as much as I can."