“I am saddened to hear of the death of His Highness Sheikh Khalifa bin Zayed Al Nahyan, President of the United Arab Emirates and Ruler of Abu Dhabi,” she said.
“Your distinguished brother devoted his life to serving the people of the United Arab Emirates and his relationship with its allies and friends.
“He will be long remembered by all who work for regional stability, understanding between nations and between faiths, and for the conservation cause.
“I offer Your Highness my sincere condolences and I extend my sympathy to the people of the United Arab Emirates.”
The queen enjoyed a close relationship with Sheikh Khalifa that was forged over several state visits.
During the course of her 70-year reign, the 96-year-old British monarch visited the UAE in 1979 and 2010
Sheikh Khalifa also came to the UK twice on formal state visits.
The first occasion was in 1989 as part of a four-day visit by the UAE Founding Father, the late Sheikh Zayed bin Sultan Al Nahyan.
The second occasion came 24 years later in 2014, when Sheikh Khalifa visited as President.
The queen's message of condolence came as concerns swirl over her own health. She missed the state opening of the UK Parliament on Wednesday for only the third time since she acceded to the throne in 1952, sparking rumours the country may be on the cusp of an unofficial second Regency period.
In February, she was also laid low and forced to miss several engagements after contracting coronavirus.
Her health struggles have been infelicitously timed, given 2022 is the year of her platinum jubilee. However, more auspiciously, on Friday she made an appearance at the Royal Windsor Horse Show, where one of her ponies was named supreme champion.