"I think he's been very polite so far this year, I think he needs to toughen up," Whitmarsh told reporters after the Mexican finished a disappointing 11th in Sunday's Chinese Grand Prix in Shanghai.
"I think he's been generous in allowing people past him. He was a bit more robust today."
Perez had a coming together with Lotus's Kimi Raikkonen on the track on lap 16, with the usually glacial Finn sufficiently exercised to exclaim heatedly over the team radio about the youngster's behaviour.
The incident damaged Raikkonen's front wing and prevented the 2007 champion challenging for the victory, eventually finishing second behind Ferrari's Fernando Alonso.
Stewards looked at the evidence and decided to take no further action rather than punishing Perez for this weekend's race in Bahrain.
The Mexican, who moved from Sauber at the end of last season as replacement for departed Lewis Hamilton, has scored two points in three races so far. Team mate Jenson Button was fifth on Sunday and has 12 points to his credit.
"I think it was robust. I've seen people weave more than that, if that's the assertion. He was doing his job, he was racing," smiled Whitmarsh of his driver's actions.
Perez's car was also damaged by the coming together but Whitmarsh said he had told the 23-year-old that he supported what he had done.
"You've got to be out there racing and that means sometimes you've got elbows," he said. "It's right that you've got to be robust without being dirty. And I think he was robust."
McLaren have been struggling to get their car up to speed after ending last year as the fastest team but starting this season some way off the pace with a new design instead of a simple evolution.
Perez has also had to contend with a world champion team mate, who managed to deliver far more points than the car deserved on Sunday, in a top team where the drivers are under close media scrutiny.
Whitmarsh said McLaren had no doubts about Perez's talent.
"With these sorts of tyres that are very fragile, with a car that's not quite there and tricky racing, I think he did a reasonable job but he's not satisfied with himself and nor should he be.
"This won't go down as his best weekend of the year."
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