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Police said an anonymous phone call led them to the wooden object, known to some as the Church of the All Saints, which was recovered from a bin outside their office.
The 40cm by 32cm icon was identified by the Russian media as one of the most valuable of the missing items, which, in total, are worth an estimated $100 million (£50 million).
Mikhail Piotrovsky, the director of the Hermitage since 1992, suspects the theft of the mainly silver and enamel museum pieces from the Middle Ages and 19th Century, was an inside job.
The exhibits were not on display in the museum but instead kept inside a locked storeroom, which only a few people had access to. Their disappearance was only discovered after an internal audit.
Valery Vekhov, a police spokesperson, said: “The caller said that at 21 Ryleyeva Street one of the Hermitage items would be in one of the rubbish bins.
“Investigators found the icon of the Church of All the Saints in a good condition but with the icon and its frame separated.”
Police have said that theft could have taken place at any time in the last 30 years, or that the art pieces were simply mislaid among the Hermitage’s three million possessions.
“The icon is now in the Hermitage, where it will be examined and officially identified,” said Ms Vekhov.
“It is possible someone took this icon earlier and then decided to get rid of it, being scared of the publicity that has surrounded the case.”
None of the items was insured because they were in storage. The museum estimates the value of the 221 objects at $5 million, but art experts who have seen the full list told the newspaper Izvestia that the market value was 20 times that.
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