With the recent discovery in Munich of €1bn (£860m) worth of art looted by the Nazis, and the forthcoming release of a feature film, starring George Clooney, based on the exploits of the Monuments Men, it is a fitting time to recall how fortunate we are that so much art survived the second world war. The Nazi art theft division, the ERR (Einsatzstab Reichsleiter Rosenberg), was responsible for the theft of around 5m works: from the Louvre, the Uffizi and countless churches, galleries and homes. From headline-grabbing works like Michelangelo's Bruges Madonna to the most frequently stolen artwork in history, Jan van Eyck's Adoration of the Mystic Lamb, both of which feature in the Clooney film, to lesser-known gems that nevertheless held a place in the hearts of museumgoers or families, the story of art looting during the second world war is a tree with countless roots. Each masterpiece has its own history, a provenance ripe with intrigue. Few of the individual stories have been told, fewer still in depth.

Among the many enduring mysteries of this periodis the fate of the world's most famous painting. It seems that Leonardo da Vinci's Mona Lisa was among the paintings found in the Altaussee salt mine in the Austrian alps, which was converted by the Nazis into their secret stolen-art warehouse.

The painting only "seems" to have been found there because contradictory information has come down through history, and the Mona Lisa is not mentioned in any wartime document, Nazi or allied, as having been in the mine. Whether it may have been at Altaussee was a question only raised when scholars examined the postwar Special Operations Executive report on the activities of Austrian double agents working for the allies to secure the mine. This report states that the team "saved such priceless objects as the Louvre's Mona Lisa". A second document, from an Austrian museum near Altaussee dated 12 December 1945, states that "the Mona Lisa from Paris" was among "80 wagons of art and cultural objects from across Europe" taken into the mine.

The Louvre has remained strangely silent about the whereabouts of its treasures during the war. But after years refusing to comment, it finally admitted that the Mona Lisa had indeed been in the Altaussee mine.

Why, then, was there no record of it? The only wartime documents available about the Mona Lisa say that on 27 August 1939 it was packed in a specially-marked crate, tailor-made in 1938, of double-thick poplar wood. Along with other artworks from French national museums, it was sent for storage, first to Chambord Castle in the Loire Valley. On 5 June 1940, it was transferred to Chauvigny on a cushioned stretcher in the back of an ambulance, which had been sealed to keep the humidity constant (the official who accompanied the painting arrived nearly asphyxiated from the lack of circulation in the sealed vehicle). In September, it moved again, to the Ingres Museum in Montauban, before a final move to Montal in 1942. According to the Louvre, the Mona Lisa was not part of the majority of works from its collection eventually stored at Château de Pau at the foot of the Pyrenees.

The last document the Louvre shared with scholars listed the safe return of the Mona Lisa to Paris on 16 June 1945. That's the same day the first of the Altaussee treasures were carried out of the mine. Unless that particular painting had been secretly removed earlier, it could not have been returned to Paris as early as the 16 June. Whether or not it was in Altaussee, a gap of nearly three years – from 1942 to 45 – remains undocumented.

The Louvre later altered its story, claiming that the version of the Mona Lisa that had been returned from the mine was an excellent copy, not by da Vinci, but painted within a generation of his death. A number of such copies exist. Was one of these found at the mine but reported by no one?

The Louvre now states that the copy of the Mona Lisa found at Altaussee was among several thousand works assembled at the Musées Nationaux Récupération – works whose owner could not be traced. This Mona Lisa copy was marked MNR 265 on the list. After five years passed with no owner coming to light, the copy was presented to the Louvre for indefinite safekeeping. From 1950 until recently, it hung outside the office of the museum's director.

Piecing together the facts, let's try to infer what really happened. The Mona Lisa would certainly have been a key target for Nazi art hunters: the ERR, Hitler himself, and the art fiend and Nazi number two, Hermann Göring. The Nazis would have sought the Mona Lisa without rest, demanding it be handed to them upon their entry to Paris, and hunting it down if it were not. Since near-identical copies of Leonardo's painting exist, it would have been strategically advisable that one be placed in that specially-marked wooden crate labelled "Mona Lisa", and shipped for storage while the original was craftily hidden away. The ERR would then chase what they believed to be the original Mona Lisa, in the crate marked as such, and upon capturing it, send it to Altaussee for storage. All the while, the original was in hiding, probably never having left Paris, officially resurfacing on 16 June 1945.

This is the only way to explain how the "Mona Lisa" – restitution number MNR 265, which now hangs in the Louvre's administrative offices – did return from Altaussee. It also explains why the Mona Lisa was not noted in all of the records related to Altaussee – some officers recognised that the Altaussee painting was a copy, while others thought it the original.

The kidnap of that copy preserved the real Mona Lisa from the Nazi art hunters, who might otherwise have wrought unimaginable damage in their search for the hidden original.

This article was adapted from Charney's book The Thefts of the Mona Lisa: On Stealing the World's Most Famous Painting.