King Charles and the Queen Consort received a message of condolence on behalf of the people of Northern Ireland from the speaker of the Stormont Assembly Alex Maskey.
The message was delivered in the Throne Room at Hillsborough Castle in a ceremony which was attended by invited guests, representing the Northern Ireland community.
Ahead of the message of condolence, the King and Queen Consort held a private audience with the new Northern Ireland Secretary Chris Heaton-Harris.
They are also met leaders of the five main political parties as well as Mr Maskey.
The speaker of the Stormont Assembly Alex Maskey described how the Queen had been part of efforts to build peace in Ireland.
In a message of condolence on behalf of the people of Northern Ireland, he said the Queen had not been "a distant observer" in the transformation and progress of relationships among the people of the country.
He said the monarch had "demonstrated how individual acts of positive leadership can help break down barriers and encourage reconciliation".
Mr Maskey added: "She showed that a small and insignificant gesture - a visit, a handshake, crossing the street or speaking a few words of Irish - can make a huge difference in changing attitudes and building relationships."
The Queen's recognition of both British and Irish traditions, as well as the wider diversity of the community was "exceptionally significant".
He added: "In all of this she personally underlined that one tradition is not diminished by reaching out to show respect to another."
In his reply to the message of condolence on behalf of the people of Northern Ireland King Charles III, said: "On behalf of all my family, I can only offer the most heartfelt thanks for your condolences.
"I am here today at a time of great personal sorrow as we mark the death of my beloved mother, after a life most faithfully dedicated to the duty to which she had been called.
"It is fitting that we should meet at Hillsborough, which my mother knew so well, and in whose beautiful rose garden she always took such pleasure.
"In the years since she began her long life of public service, my mother saw Northern Ireland pass through momentous and historic changes.
"Through all those years, she never ceased to pray for the best of times for this place and for its people, whose stories she knew, whose sorrows our Family had felt, and for whom she had a great affection and regard.
"My mother felt deeply, I know, the significance of the role she herself played in bringing together those whom history had separated, and in extending a hand to make possible the healing of long-held hurts.
"At the very beginning of her life of service, The Queen made a pledge to dedicate herself to her country and her people and to maintain the principles of constitutional government.
"This promise she kept with steadfast faith. Now, with that shining example before me, and with God's help, I take up my new duties resolved to seek the welfare of all the inhabitants of Northern Ireland.
"During the years of my mother's reign, it has been a privilege to bear witness to such a devoted life. May it be granted to us all to fulfil the tasks before us so well."
King Charles was greeted by cheering crowds as he arrived at the Northern Ireland village of Royal Hillsborough as part of his tour of the UK.
The King performed a walkabout and stopped to greet and talk to many people in the crowds.
Charles and Camilla then stopped to view the many tributes to the Queen at the front of Hillsborough Castle.
Crowds lined the streets of Royal Hillsborough from the early hours of Tuesday ahead of the King's first visit to Northern Ireland as monarch.
King Charles III is in Northern Ireland as part of a tour of the UK ahead of the Queen's state funeral.
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