In a statement, the palace said the queen had "reluctantly accepted medical advice" to stay home.
"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 statement said.
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"The queen sends her warmest good wishes to the people of Northern Ireland and looks forward to visiting in the future," it added.
Elizabeth, who is 95, had been expected to begin a two-day visit to Northern Ireland on Wednesday.
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It is unclear why she was given medical advice to rest, instead, and whether the advice will affect her attendance at events surrounding the COP26 climate crisis conference, which launches later this month.
According to the British newspaper The Guardian, the queen is resting at Windsor Castle, where she hosted business leaders and politicians, including Prime Minister Boris Johnson, on Tuesday evening after the government’s investment summit.
It has been nearly seven months since the death of Prince Philip, who was married to the queen for more than 70 years.
His passing came as the royal family confronted fresh challenges, including intense publicity around the departures of Prince Harry and Meghan, the Duchess of Sussex, from their royal duties.