The presenting duo faced criticism from some people on social media after they appeared inside Westminster Hall on Friday without having taken part in the public queue.
Programme bosses said in a statement that Holly and Phillip had attended to film a segment due to air during Tuesday’s show and were there to report on the event as media.
They said: “Hello everyone, we would like to clarify something. 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 have been able to bypass the queue and access Westminster Hall since its doors opened to the public on Wednesday.
In the days since, the queue has swelled in size and at one time reached a wait time of “at least 24 hours”.
The lying in state is also being broadcast live and 24/7 by a number of broadcasters including the BBC and Sky News.
Other famous faces have also paid their respects to the Queen ahead of her funeral.
The former England captain looked emotional as he finally made it inside Westminster Hall to view the monarch’s coffin on Friday evening after queuing for 13 hours.
Live footage appeared to show the him wiping away tears as he approached the coffin.
Speaking to reporters after the viewing, the 47-year-old star said it had been an “special” but “difficult” day.
Good Morning Britain host Susanna Reid said she had queued for seven hours and 20 minutes to see the lying in state.
The Good Morning Britain anchor attended the historic event on Thursday with her mum, Sue, and said she had “experienced a moment in history”.