The 95-year-old monarch was meant to be travelling to Northern Ireland for a two day trip, which was due to begin on Wednesday. She is said to be in “good spirits” and “disappointed” that she is no longer able to go.
The Queen was due to attend a church service to mark 100 years of Northern Ireland in Armagh city.
A Buckingham Palace spokesperson said: “The Queen has reluctantly accepted medical advice to rest for the next few days.
“Her Majesty is in good spirits and is disappointed that she will no longer be able to visit Northern Ireland, where she had been due to undertake a series of engagements today and tomorrow.
“The Queen sends her warmest good wishes to the people of Northern Ireland, and looks forward to visiting in the future.”
The decision is understood to not be related to coronavirus, the Press Association reported.
The centenary service is due to take place on Thursday and the Catholic primate of All Ireland, Archbishop Eamon Martin, will attend along with the heads of the Church of Ireland, the Presbyterian Church in Ireland, the Methodist Church in Ireland and the Irish Council of Churches.
Irish President Michael D Higgins has declined an invitation to the service, a move that was criticised by unionist politicians.
The Queen has had a busy few days and held two audiences yesterday via video link from Windsor Castle.
Last night, she welcomed business leaders, presidential envoys and tech entrepreneurs to the castle for a reception following a Government investment summit.