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Mona Lisa (right) and the original found underneath (left)
He spent 10 years analysing the artwork and used a multispectral imaging camera to make the discovery, which has led to a digital recreation of the original being made.
Mr Cotte, who was given access to the painting in 2004, says that an earlier image was hidden by Leonardo underneath his masterpiece.
The results shatter many myths and alter our vision of Leonardo’s masterpiece forever
One acclaimed art historian has claimed the original artwork is of Pacifica Brandano.
Mr Cotte said: “The results shatter many myths and alter our vision of Leonardo’s masterpiece forever.
“When I finished the reconstruction of Lisa Gherardini, I was in front of the portrait and she is totally different to Mona Lisa today.
“This is not the same woman.”
Pacifica Brandano, who is believed to be the woman underneath the Mona Lisa
The Mona Lisa is Leonardo da Vinci’s most celebrated piece
He said the digital recreation was a “perfect match for the historical record”.
The documentary claims the subject is Pacifica, who was the mistress of Leonardo’s patron Giuliano de Lorenzi de Medici.
The Mona Lisa has attracted international intrigue
Mr Cote used his own Layer Amplification Method on the masterpiece.
It works by “projecting a series of intense lights” onto the painting, Mr Cotte said.
A camera then takes measurements of the lights’ reflections and from those measurements, Mr Cotte said he is able to reconstruct what has happened between the layers of the paint.
The Duchess of Cornwall with The Mona Lisa in 2013
“We can reconstruct all the chronology of the creation of the painting.”
However not everyone is convinced about the original.
Martin Kemp, Emeritus Professor of the History of Art at the University of Oxford, said: “They [Cotte’s images] are ingenious in showing what Leonardo may have been thinking about.
“But the idea that there is that picture as it were hiding underneath the surface is untenable.
“I do not think there are these discreet stages which represent different portraits. I see it as more or less a continuous process of evolution. I am absolutely convinced that the Mona Lisa is Lisa.”
The Louvre Museum has declined to comment on his claims because it “was not part of the scientific team”.
Instead of the famous, direct gaze of the painting which hangs in the Louvre Museum in Paris, the image of the sitter also shows no trace of her enigmatic smile, which has intrigued art lovers for more than 500 years.
Will Gompertz, Arts Editor for the BBC said he was “sceptical”.
He added: “It’s perfectly common for an artist to overpaint an image as it is for a client who’s commissioned that artist to ask for changes.
“So it’s not surprising that there are those underpaintings on the Mona Lisa.”