The presenters spoke out on the ITV show earlier this month after being pictured in what looked like a fast-track queue to view the Queen's lying in state at Westminster Hall, saying they would never queue jump and were there purely in a work capacity.
The broadcasting watchdog confirmed to Yahoo that the complaints related to Willoughby and Schofield's explanation of their prior broadcast from Westminster Hall during the mourning period for Her Majesty.
Many people were fuming after the TV stars were seen at the lying in state, where thousands of members of the public queued for hours to pay their respects.
And a Change.org petition to have them axed from television has reached more than 77,000 signatures.
Addressing the furore, Willoughby said in a statement on the show: "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 haven't been able to visit Westminster in person.
Watch: Holly Willoughby and Phillip Schofield attend the Queen's lying in state
"The rules were that we would be quickly escorted around the edges to a platform at the back. In contrast, those paying respects 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 we totally understand the reaction.
"Please know that we would never jump a queue."
ITV chief executive Dame Carolyn McCall has also said the presenters did "nothing" wrong.
Speaking at the RTS London Convention she said the pair had accreditation and were sent by This Morning to do a piece.
Read more: Eamonn Holmes jokes about queue-gate row
She said Willoughby and Schofield had been "very misrepresented".
Watch: Piers Morgan defends Holly Willoughby and Phillip Schofield over queue controversy