After months of speculation, the British driver confirmed his departure from his team of 14 years in September, and Whitmarsh has revealed that the pair have had several "emotional moments" since Hamilton announced his McLaren exit.
"I think he has on occasions [regretted it]," Whitmarsh told the official Formula 1 website.
"He's made that decision and he has to live with that decision. I have known him since he was 11 and worked with him since his teens and I know we will both be very emotional after Brazil.
"We have had one or two emotional moments since the decision was taken and I believe, but you must ask him, that we have a very good relationship."
Hamilton will drive for Mercedes from the beginning of the 2013 season.