The Mexican driver joined McLaren for this year, replacing Lewis Hamilton after spending two seasons with Sauber.
Perez claimed at the end of last year that he saw no reason why he could not immediately fight for the title with McLaren, but its car struggles have meant he has scored just two points in the first two races.
Whitmarsh praised Perez's approach to McLaren's problems, and says his new driver is yet to put a foot wrong.
"He has done a solid job," said Whitmarsh. "It is easy to get rattled coming to a team like McLaren when you don't have a quick enough car.
"He is an intelligent guy. He is incredibly young but again in my mind he has not put a foot wrong."
Perez said recently that he had no regrets about his move to McLaren despite the team's form so far, and Whitmarsh reckons it is a blessing to have two drivers with Perez and Jenson Button's attitude.
"He is a team player," he said. "There are a few glimmers of positive things but we haven't started well.
"I am very, very blessed at the moment with the drivers we have got and their attitude and approach, and they are powering through."
Sergio Perez's recent comments that he would rather be facing his current difficulties with McLaren than winning races elsewhere certainly raised some eyebrows.
How could a youngster without a victory under his belt be embracing a struggle to get in to Q3 compared to fighting it out for a top step of the podium?
The answer comes simply from the Mexican having found somewhere that he feels is home.
He has moved on from his schooling experience with Sauber and the Ferrari Driver Academy to join what he feels is the big boy's league. He is not ashamed to call McLaren the best team in F1. And he is revelling in it.
Yes there have been difficulties - including the mistakenly early switch to slicks in Australian GP qualifying that dumped him out early - but he has kept his head down: focusing on delivering as much as he can with the machinery he has at his disposal.
In Australia it almost slipped under the radar that he finished less than two seconds adrift of Jenson Button.
Until McLaren gives him a better car, Perez knows that victory is something that can only be imagined for now.
But in talking things up, and loving the challenge he is facing, he is putting himself in the best position he can to seize that winning chance when it comes.