Silvano Vinceti, chairman of the Italian national committee for cultural heritage, said the Florence-born Renaissance artist's male apprentice and possible lover Salai was the main inspiration for the picture.
However his claim was immediately disputed by experts at the Louvre in Paris, where the painting is on display.
Salai, real name Gian Giacomo Caprotti, a young artist who worked with da Vinci for 25 years, is thought to have served as a model and muse for several of his paintings. The pair had an "ambiguous" relationship and were probably lovers, Mr Vinceti said.
Comparisons between the facial characteristics of figures from several of da Vinci's works -- such as St. John the Baptist and the Angel Incarnate - reveal striking similarities with the Mona Lisa's nose and mouth, he said.
"There are remarkable similarities," Mr Vinceti said.
What is more, Mr Vinceti said, da Vinci had left clues to the model's identity in tiny letters L and S which he and his team found painted into the eyes of the Mona Lisa.
"Close examination of a high-quality digital copy of the portrait had revealed an L for Leonardo and an S for Salai," he said.
But Vinceti's claims have been disputed by the Louvre museum.
The museum said it had carried out "every possible laboratory test possible" on the picture in 2004 and then again in 2009, and insisted that "no inscriptions, letters or numbers, were discovered during the tests."
"The aging of the painting on wood has caused a great number of cracks to appear in the paint, which have caused a number of shapes to appear that have often been subject to over-interpretation," the Louvre said.
The museum also said Mr Vinceti had made his claims without having had access to the painting itself.