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 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% 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."
Red Bull's Sebastian Vettel will win the drivers' title for the third year running if he can finish 15 points ahead of Ferrari's Fernando Alonso in the 56-lap race at the Circuit of The Americas in Austin, Texas.