The established painting of Saint Jerome Writing adorns the Oratory of Saint John's Co-Cathedral in Valletta, the Maltese capital.
"He did a great part of the composition," Lapucci said. "The saint is all his, as are the table top and the objects."
She said that "the composition was finished off by someone else" with "subsequent restorations" in the 18th and 19th centuries.
Lapucci said that one of the reasons Caravaggio might have left this work unfinished is that he moved on to paint the final version.
Discovery disputed
But Caravaggio experts said the work Lapucci examined was not of the same quality of a Caravaggio original.
Keith Sciberras, art history professor of University of Malta and a Caravaggio expert, said: "It does not have his vigor, it does not have his brush work ... It does not have the spirit of Caravaggio in it."
Maurizio Marini, a leading Caravaggio scholar in Italy, said that the face of the saint was too coarse to have been painted by Caravaggio.
"Everything can be said of Caravaggio, but not that the quality of his work was scarce," said Marini.
The painting that Lapucci examined belongs to a private collector in Malta.
The collector had sent it to her lab to have it cleaned up for an exhibit featuring the two versions side-by-side as part of events marking the 400th anniversary of Caravaggio's visit to the island in 1607-1608.