"Ferrari have done a fantastic job and we and Williams have under-performed, " Whitmarsh said.
"He's perfectly poised to develop into a world championship challenger, " Whitmarsh said in a statement.
Whitmarsh told reporters he believed the judges were "confident of our facts" following the hearing.
Whitmarsh said McLaren did not make a habit of blaming their drivers in public.
However, Whitmarsh believes Hamilton will rebound at the next grand prix in Spain.
McLaren team principal Martin Whitmarsh praised Perez's "giant-killing performances" and "podium finishes" this season.
McLaren team principal Martin Whitmarsh paid tribute to Vettel's drive at the Yas Marina circuit.
Whitmarsh said they would be making some minor changes to the car for the Bahrain Grand Prix.
"What teams do with their drivers should be for the teams to decide, " said Whitmarsh at the Hungaroring.
But Whitmarsh has laid the responsibility at Ryan's door and we have to take him at face value.
New team principal Whitmarsh also confirmed on Thursday that he offered to quit.
Head's view was backed up by McLaren's managing director Martin Whitmarsh, who insisted his team would not support "handicapping".
Whitmarsh was effusive about the pair's relationship in comments on the team's website.
"Look at the budget, " McLaren team boss Martin Whitmarsh said before Sunday's race.
"He's come with a point to prove, " said McLaren team boss Martin Whitmarsh.
Why would Whitmarsh or Dennis need to get involved when going to see the stewards is a very straightforward occurrence?
Meanwhile, McLaren said Ron Dennis will step down as team principal on 1 March, to be replaced by Martin Whitmarsh.
"We haven't had word from freight yet and we've got to get the cars back, " McLaren boss Martin Whitmarsh said.
Whitmarsh hailed the "maturity" of the 33-year-old, and admitted he had resisted calls to stop the duo competing against each other.
"You certainly don't want a repeat of what happened, " Whitmarsh told the BBC after Friday practice at the Hungarian Grand Prix.
Whitmarsh was quick to praise Hamilton and suggested that the points Hamilton picked up could become invaluable later in the season.
But, after McLaren boss Martin Whitmarsh said Fota was "open to finding a solution if we can", Mosley's stance has also calmed.
Whitmarsh also passed on his thanks to the departing Hamilton, whose performances wrote "a huge chapter" in his and the team's life.
"These tires are very, very challenging, " McLaren team boss Martin Whitmarsh said.
"There is no doubt now that Kers is an advantage, " said Whitmarsh.
Whitmarsh, who was previously just the CEO of the F1 operation, said there were times both he and Dennis did not see eye-to-eye.
McLaren's Martin Whitmarsh wants a solution which "may or may not include a budget cap, but which ideally would not encompass a two-tier regulatory framework".
He was backed by McLaren team boss Martin Whitmarsh, whose drivers Jenson Button and Lewis Hamilton both had tire troubles on the Bahrain International Circuit.
Whitmarsh said the MP4-19 was an evolutionary step forward from the MP4-18's design, but had a new engine and incorporated a lower degree of technical risk.
BBC: SPORT | Motorsport | Formula One | McLaren happy with new car
Whitmarsh is confident the MP4-19 will be ready to do battle with rivals Ferrari and Williams when the season gets under way in Australia on March 7.
BBC: SPORT | Motorsport | Formula One | McLaren happy with new car
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