Meghan, who is the late Senator’s daughter, was teary in several moments during the ceremony, but when she she stepped up to her father’s coffin after her mother, Cindy, she seemed to shake.
She touched the coffin with her right hand, leaning on it for support before walking away while sobbing.
Meghan was clearly close to her father and when the veteran passed away on Saturday she shared a heartbreaking statement and tribute on Twitter.
She wrote: “All that I am is thanks to him.
“Now that he is gone, the task of my lifetime is to live up to his example, his expectations, and his love.
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“My father is gone, and I miss him as only an adoring daughter can.
“But in this loss, and in this sorrow, I take comfort in this: John McCain, hero of the republic and to his little girl, wakes today to something more glorious than anything on this earth.”
At the Arizona State Capitol building, John McCain’s wife, Cindy, and their other two children were also present to honour the Senator.
Cindy was the first one to walk up on stage, patting the coffin and leaning over to “kiss her husband” one last time.
She also dedicated a tweet to her husband, in which she said that her “heart is broken”.
She added: “I am so lucky to have lived the adventure of loving this incredible man for 38 years.
“He passed the way he lived, on his own terms, surrounded by the people loved, in the place he loved best.”
Cindy was escorted by her other two sons, Jack, who was wearing his white Navy dress uniform, and Jimmy, in his Army dress uniform.
Senator McCain’s body will lie in Arizona before his final journey to the US Naval Academy in Washington DC.
On Friday, there will be a ceremony in his honour at the Capitol building.
The following day, a funeral will take place at Washington’s National Cathedral and he will be buried at Hospital Hill at Naval Academy Cemetery on Sunday.