Former world champions McLaren, now run by American Zak Brown, have not won a grand prix since 2012 or a title for a decade.
"Martin worked for McLaren for many years, but has been outside the business for some time and is not part of our future," a spokesman said ahead of this weekend's French Grand Prix.
"What he said was ill-judged and ill-informed in our view but he is entitled to his opinion.
"There are high expectations in the team and we won't compromise those high expectations. Everyone at McLaren is working tremendously hard and is focused on the future, not the past," he added.
A report in Britain's Daily Mail newspaper last week had quoted Whitmarsh, who left the team in 2014, as saying the former world champions needed change.
They are currently fifth overall, having ended an unsuccessful three-year partnership with Honda and switched to Renault engines.
The paper said management were "facing a revolt from disgruntled staff" who had expressed their frustration to Whitmarsh.
"I love the team and I am desperately sad to see what it has become," the former principal told the paper.
"It needs a big change of approach. There is too much politics between the main figures. I think a number of them have to go. I have explained my view to (shareholder) Mansour (Ojjeh) and it is for the shareholders to decide what to do."
(Reporting by Alan Baldwin, editing by Jason Neely)
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