"It has invested heavily in the past three years and has not achieved the results it expected. But it is doing everything in its power to win," he told El Pais newspaper.
"Hamilton has seen this potential that has not yet materialised.
"What is clear," added the Italian, "is that McLaren has lost a tremendous asset.
"After Fernando (Alonso), Vettel and him are the fastest ones."
Meanwhile, Domenicali defended Alonso's number 2 teammate Felipe Massa, amid intense speculation in Korea that the 31-year-old will be retained in 2013.
"There is no evidence," he said, "that he is still suffering either medically or mentally from the accident he had three years ago.
"I think what happened is that he suffered more than his teammate with the cars we have designed lately.
"Another element to consider is that it is not easy for anyone to have someone like Fernando as your teammate. You have to be very mature to accept how good he is.
"That's something we experienced with Schumacher as well -- when we had someone next to him who is able to recognise that Schumacher was faster, everything was perfect.
"When he (the number 2) tries to prove that he is better and he does not, problems appeared," added Domenicali.