According to the monarch, her father George VI ordered for the jewels to be hidden in the grounds of Windsor Castle, where they were buried, hidden in a biscuit tin.
The most precious jewels - the Black Prince's Ruby and St Edward's Sapphire - were even removed from the Imperial State Crown and kept separately in the biscuit tin "in case of emergency".
The documentary is part of the Royal Collection Season, a major partnership between the BBC and Royal Collection Trust.
The Queen did not know the full details of the story until she was told by royal commentator Alastair Bruce, who presents the documentary due to be broadcast this Sunday. "Telling her seemed strangely odd".
The Queen rides in the Gold State Coach after her coronation
"I think that the queen must understand that, as we do as producers, that it's been 65 years since we've had a coronation and the British public have been aware of the Crown Jewels, but think they've become the best known and least understood symbols of the country as a result of that amount of time not being in use, and maybe that's what led her to do it now".
And the trap door used to access the secret area where the artefacts were stored still exists today.
In a rare television interview, Britain's Queen Elizabeth II has shared private thoughts about her coronation, describing one of the crowns she wore at the ceremony as so heavy "your neck would break off".
In the documentary the Queen also talks about the amusing trials and tribulations of being head of state.
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The documentary will reportedly show never-before-seen footage throughout, with one clip featuring a four-year-old Prince Charles and younger sister Anne playing underneath the Queen's long robe.
The Queen, 91, told the broadcaster her diamond-encrusted Imperial State Crown, which weighs 1.3 kilograms, was "very unwieldy".
She also said the golden ceremonial carriage used for her coronation was "horrible".
"Fortunately, my father and I have about the same sort of shaped head", the queen said. "He said, 'Do you realise you have the real Crown?' And I said, 'I do realise that".
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Her coronation, the following year, was watched by 27 million people in the United Kingdom and millions of others from around the world. "I mean it just remains on", the Queen notes.
"I remember one moment when I was going against the pile of the carpet and I couldn't move at all", she says.
The documentary "The Coronation" is part of the Royal Collection Season and will be screened in the United Kingdom on BBC One at 8pm local time on Sunday.
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