The two, who were walking down the Buckingham Palace garden, were speaking about the trees she planted for her children when amidst the conversation a helicopter hovering in the air made it hard for the Queen to talk with all the noise.
"Why do they always go round and round when you want to talk?" the Queen says.
The film, "The Queen's Green Planet", which will be broadcast on ITV in Britain on April 16, highlights her work trying to build a global network of protected forests, The Queen's Commonwealth Canopy.
Hollywood actress Angelina Jolie, and her six children, will also feature in the ITV documentary, which will air next Monday.
The Queen cracked a rare public joke on a stroll with Sir David Attenborough, poking fun at the noisy aircraft favoured by United States presidents. "They have known each other a long time and because of that we see quite surprising things", she added.
"It might easily be, yes." she said.
When the pair come across a sundial positioned in the shade which Sir David points out, the Queen seems surprised at the oversight.
"Isn't it good, yes", the queen says, before flashing a wide grin at a person standing off camera. Her son Prince Charles has previously admitted to talking to plants and trees to help them grow, but recently joked that rather than taking the softly-softly approach, "now I instruct them instead".
Twitter users also went wild at the sight of the Queen and Attenborough chatting and making jokes. "Somebody sat on it, I think at a garden party", she said.
"The Queen's Green Planet" is set to air on United Kingdom broadcaster ITV later this month.
The pair stroll through the 40 acre gardens with the Queen telling the story of some of the trees planted by family members or for her children.