"There is no implication that Lewis lied to the stewards," team principal Martin Whitmarsh told reporters at the Malaysian Grand Prix.
"I think he answered the questions that were put to him in an honest manner but, according to the stewards, the team should have provided a fuller account of what happened."
Hamilton had been promoted to third place in Melbourne after stewards ruled at a post-race hearing that Toyota's Jarno Trulli had overtaken him against the rules while the safety car was deployed.
Today the same stewards met again at Sepang to consider a 'new element'. Hamilton and McLaren were ruled to have provided deliberately misleading evidence and were excluded from the classification.
The governing International Automobile Federation (FIA) later made available a recording and transcript of a radio conversation in which the team is clearly heard telling Hamilton to "allow the Toyota through".
The FIA said that, and a media interview, contradicted what Hamilton and team manager Dave Ryan had told stewards after the race.
"Both the driver and the team manager stated that no such instruction had been given," the FIA said. "The race director specifically asked Hamilton whether he had consciously allowed Trulli to overtake. Hamilton insisted that he had not done so."
The FIA said the stewards now "felt strongly that they had been misled by the driver and his team manager."
"There was no lie in that hearing," said Whitmarsh, giving McLaren's version of events.
"We the team made a mistake in that we did not provide a full account of a radio conversation that we believed was being listened to in any case."
Whitmarsh said that Trulli had skidded off the track while in third place and while the safety car was deployed. Hamilton, fourth, had gone past as he was allowed to.
However McLaren could not see what had happened to the Italian and feared that Hamilton might be penalised for illegally overtaking - as he was last year when stewards stripped him of victory in Belgium.
"There was understandably concern in the team that he had passed Trulli under a safety car," said Whitmarsh. "We didn't know Trulli was right off the circuit and Lewis was asked to give back the place.
"We thought that was the safest thing to do. Once that instruction was given to Lewis, he didn't agree.
In the radio transmission, Hamilton can be heard saying "I just let him past" and then soon after: "I don't have to let him past, I should be able to take that position back, if he made a mistake."
Whitmarsh said McLaren had then asked race control for permission to retake the place but received no answer. So the matter was taken to the stewards.
"At the stewards meeting, we mistakenly believed that the stewards were aware of that radio conversation," said Whitmarsh. "The stewards now believe that we weren't explicit enough about that radio conversation.
"We regret that and it was a mistake by the team."