The Queen called Obama's bevy of choppers "over the top", meaning the Secret Service had to rethink their plans to land about six aircraft in the 300-year-old gardens of her main residence.
"It was a write-off and the Queen was not amused," 'Daily Express' quoted a royal source as saying.
"Her Majesty refused to back down and said, 'three helicopters only'. The Secret Service had to go away and think about their plan. The President's officials were told that the Queen regarded Windsor Castle as her family home and the most important of all royal residences," the report said.
The Queen, whose 90th birthday was celebrated recently, said there was no chance Obama's extensive security backup would be accompanying him to Windsor Castle.
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Her insistence came after Obama's helicopters damaged the grass when half a dozen of them landed during his last visit in 2011.
The engines' heat scorched the grounds and the wheels left divots in one of the UK's oldest lawns, planted during the reign of Queen Anne in the early 1700s.
An insider said US aides refused to change their plans on security grounds but came around to the Queen's wishes eventually.
"They said they needed to be within reach of the president at all times. They also wanted guards posted inside the dining hall when he had lunch with the Queen," the insider said.
" But Her Majesty refused to back down and said, 'three helicopters only'. Eventually the President's aides accepted her wishes," the report said.