A spokeswoman for the Paris prosecutor said: "The owners just discovered the theft but it could have taken place any time between late July and late August."
"We're talking about very, very good wine worth between €500 and €1000 per bottle," she said. "It appears they made their getaway back down the catacombs. The judicial police of the 3rd district have launched an investigation, searching both the cellar and the tunnels below."
The cellar was under a block of flats in Rue d'Assas, which runs right next to the Luxembourg gardens.
A network of about 240km of underground tunnels forms a labyrinth 20m beneath Paris, with only a small section open to the public at an official visitors' site in southern Paris.
The ambient temperature in the dank narrow passageways is about 15C.
Once quarries, their limestone was excavated in the boom of the late Middle Ages, providing the stone that became Notre Dame cathedral and the Louvre.
After entire streets caved into the honeycomb in the late 18th century, Louis XVI ordered inspectors to chart and fill chambers. Many were turned into ossuaries, with the bones of approximately six million people transferred there from Parisian cemeteries for public health reasons.
The stench from ground-level burial sites had become intolerable.
Tales abound of the catacombs' secrets. In fiction, The Phantom of the Opera's title character and Les Misérables' Jean Valjean both haunted these tunnels, and in reality they were used by the French Resistance in World War II, while the Nazis built a bunker in the 6th arrondissement - not far from the burglary site.
Entering the non-official galleries has been illegal since 1955, but schoolchildren and partygoers have been known to access them at secret entry points, mainly wells under crypts, hospitals, bars and restaurants. Those who do so are nicknamed "cataphiles".
In 2004, police stumbled upon an entire cinema underground, protected by recorded sounds of growling guard dogs. The cinema's 20 seats had been carved into the stone itself.