The pair were criticised on social media after they appeared inside Westminster Hall on Friday without taking part in the public line.
Programme bosses later said in a statement that the hosting duo had attended to film a segment for Tuesday’s show.
As This Morning returned to ITV after the state funeral on Monday, the pair acknowledged the backlash but stressed they had “respected” the rules set for the media.
During the special episode reflecting on the days since the Queen’s death, Willoughby said in a voiceover: “Like hundreds of accredited broadcasters and journalists we were given official permission to access the hall.
“It was strictly for the purpose of reporting on the event for millions of people in the UK who have not been able to visit Westminster in person.
“The rules were that we would be quickly escorted around the edges to a platform at the back.
“In contrast, those paying respect walked along a carpeted area beside the coffin and were given time to pause.
“None of the broadcasters and journalists there took anyone’s place in the queue and no one filed past the Queen. We of course respected those rules.
“However, we realise that it may have looked like something else, and therefore totally understand the reaction. Please know that we would never jump a queue.”
This Morning previously addressed the visit in a statement posted on Instagram on Saturday, saying: “We asked Phillip and Holly to be part of a film for this Tuesday’s programme.
“They did not jump the queue, have VIP access or file past the Queen lying in state – but instead were there in a professional capacity as part of the world’s media to report on the event.”
Some media and MPs were able to bypass the queue and access Westminster Hall during the roughly four-day lying in state.
During that period, the queue swelled in size and at some points reached a wait time of “at least 24 hours”.
On Tuesday, Culture Secretary Michelle Donelan said around a quarter of a million people had paid their respects in person by viewing the Queen’s coffin.
The lying in state was also broadcast live and 24/7 by a number of broadcasters including the BBC and Sky News.
Good Morning Britain host Susanna Reid, 51, and David Beckham, 47, were among the famous faces who joined the public queue.