Lisa Gherardini died in Florence in 1542 and was buried in the grounds of Sant'Orsola convent, but her remains were dug up 30 years ago, telegraph.co.uk reported Monday.
Over the centuries the Franciscan convent was used as a tobacco factory and a university teaching facility but in the 1980s a redevelopment was launched to convert it into a barrack for Italy's tax police, Guardia di Finanza.
The developers had no knowledge that it was the final resting place of da Vinci's famous model - that was only discovered in 2007. During work to build an underground car park, the convent's foundations were excavated, along with the crumbling remains of graves and tombs.
The rubble was then dumped in a municipal landfill site on the outskirts of Florence.
Giuseppe Pallanti, an expert on da Vinci and author of "Mona Lisa Revealed: The True Identity of Leonardo's Model", has spent 30 years studying the archives trying to establish Lisa Gherardini's final resting place.
He is convinced her remains are interred in the dump, now a grassy mound nearly 100 feet high. "The tombs have all been lost," he said. "Sadly, when the works were carried out in the 1980s no thought was given to the historical importance of the building and its artefacts.
The prosaic end to the life of one of the best known figures in art history has only recently come to light through a fresh building project for the convent site. The Florence city council wants to turn the half-built police barracks, which has lain semi-derelict and bricked up for years, into a 23-million pound community arts centre.
Surveys of the site have shown that the site was excavated in the 1980s to such a depth that no tombs or other historical artefacts survived. Gherardini is believed to have been born in Florence in 1479. At the age of 16 she became the second wife of a wealthy silk merchant, Francesco del Giocondo, with whom she had five children.
She moved into the convent after his death, staying there for the last four years of her life. She is believed to have died in the convent at the age of 63 in 1542, according to a document unearthed three years ago by Pallanti during his research.
The portrait that came to be known as the Mona Lisa, which now hangs in the Louvre Museum in Paris, was completed by Leonardo in 1506 when she was about 24.
The arts centre is due to be completed in 2015 and Pallanti wants the authorities to incorporate some sort of commemoration of Gherardini.