Pascal Cotte said Leonardo built the painting up in layers, the last being a special glaze whose optical properties increased the illusion of a three-dimensional face. Above the glaze Leonardo painted details such as the eyebrows.
Cotte said: "That could explain why the eyebrows have disappeared – they have faded because of chemical reactions or they have been cleaned off."
He has uncovered a host of secrets about the Mona Lisa using a 240 megapixel camera. It can measure light so sensitively as to see through the top paint surface and uncover the layers below.
For example, infra-red imaging shows Leonardo moved the position of a finger on the left hand "to give a more relaxed position, consistent with the smile", Cotte said.
He said the Mona Lisa looked "totally different" 500 years ago, when it had a blue sky and the subject's skin had not yellowed.
The underlying layers of the face - painted using lead white and mercury vermillion - also show it was wider than the end result appears.
"The smile, the glance, the face were all wider," said Cotte.
But Leonardo did not change his mind half way through, he said. On top of the base layers the artist added a glazed shadowing layer to create a three dimensional effect.
"I do not say that he was successful, in reproducing a stereo-vision effect, but if you want to achieve that this is the best way to do it," said Cotte.
"But now it looks totally different to how he painted it. All the optical effects have disappeared."
He said that for Leonardo the Mona Lisa was "more than a painting, it was a challenge to reproduce real life".
Cotte's work is explained in an exhibition, The Secrets of the Mona Lisa, that opened at the Museum of Science and Industry in Manchester on Saturday.