'Under layers of dull varnish and dirt, he discovered something much more interesting than we had ever thought before. It was very, very exciting.
'We have since had experts from around the globe examine the work and it has now, formally, been attributed to Caravaggio.
'As a result of this we decided to look at Boy Peeling Fruit again, which has also now been pronounced as an original.'
The process of authentication is rigorous and has involved academics from the U.S. and Italy as well as the UK.
'Experts look at everything from the way it is painted - Caravaggio's brushstrokes are swift and accurate - through to the amount of paint used and marks on the canvas.
'Obviously it is exciting to discover the provenance of any painting, but Caravaggio died very young, at the age of just 32, and as a result there are very few original works of his in existence today,' said Miss Whitaker.
'He is an artist that people feel very deeply about. He was always very controversial, for example painting the saints with dirty feet. But he was also very humane.'
Both paintings are part of The Royal Collection, which is held by the Queen on behalf of the nation. Despite their enormous value, she is not allowed to sell them.
They are on show as part of the The Art of Italy in the Royal Collection exhibition at the Queen's Gallery, Buckingham Palace, until January 2008.
Surveyor of the Queen's Pictures, Desmond Shawe-Taylor, said the display made up an 'unsurpassable' collection of Renaissance and Baroque art, including works by Titian, Leonardo da Vinci, Raphael and Michelangelo.
'We knew we had an unimaginably great collection and unbelievably wonderful individual paintings - but I don't think anybody knew quite how good it was all together,' he said.