“The PM was in Balmoral over the weekend. It was an entirely private visit,” his official spokesman said.
The spokesman declined comment further or confirm reports Mr Johnson was accompanied by his wife Carrie and their 16-month old son Wilfred during the visit.
Watch: Who is The Queen?
It is reported this year’s visit was the 95-year-old Queen’s first opportunity to be introduced to Wilfred.
The couple last visited the Queen’s royal estate in Scotland in 2019.
Last year’s trip was cancelled due to the pandemic.
But the Queen has continued to carry out engagements this year, despite the coronavirus pandemic.
She has been staying at her private Scottish estate, where she traditionally spends her summer break.
It marked her first summer holiday at her Scottish estate following the death of her husband Prince Philip in April.
She has been joined by family members including the Duke of York and his ex-wife Sarah, Duchess of York.
Her Majesty will remain at her Aberdeenshire estate until early October.
Scotland has been a welcome retreat for the royal family since Queen Victoria’s day.
The Windsors have always enjoyed the country pursuits in the stunning setting of the Scottish Highlands.
Watch: Queen says hello to Shetland pony at Balmoral