"While our Party has bestowed upon him the nomination, it is not accompanied by unfettered license to defame those who are the best among us," McCain said in a statement Monday.
Trump's criticism of Khan after he spoke from the stage of the Democratic convention last week resurrected the billionaire developer's past comments accusing McCain of not being a war hero because he was captured in Vietnam.
"I cannot emphasize enough how deeply I disagree with Mr. Trump's statement. I hope Americans understand that the remarks do not represent the views of our Republican Party, its officers, or candidates," McCain, who has previously announced he supports Trump for president, said Monday.
In the very personal statement, McCain also paid homage to the Khan's son Humayun's sacrifice.
"I'd like to say to Mr. and Mrs. Khan: thank you for immigrating to America. We're a better country because of you. And you are certainly right; your son was the best of America, and the memory of his sacrifice will make us a better nation -- and he will never be forgotten."
McCain noted that his own son also served in the Iraq War and that McCains have been serving in the US military for hundreds of years.
"My sons serve today, and I'm proud of them. My youngest served in the war that claimed Captain Khan's life as well as in Afghanistan. I want them to be proud of me. I want to do the right thing by them and their comrades," McCain said.
"Humayun Khan did exactly that — and he did it for all the right reasons. This accomplished young man was not driven to service as a United States Army officer because he was compelled to by any material need. He was inspired as a young man by his reading of Thomas Jefferson — and he wanted to give back to the country that had taken him and his parents in as immigrants when he was only two years old.
"Captain Khan's death in Iraq, on June 8th, 2004, was a shining example of the valor and bravery inculcated into our military. When a suicide bomber accelerated his vehicle toward a facility with hundreds of American soldiers, Captain Khan ordered his subordinates away from the danger.
"Then he ran toward it."