Auditors noticed that pieces of silver and enamel, made by Russian craftsmen in the Middle Ages and 19th century, were missing during stock taking last month. The lost artworks included icons, religious works and items containing precious stones.
Police said the museum collection was so big that the pieces could have disappeared at any time in the last 30 years, but Mikhail Piotrovsky, the museum director, said he suspected the loss was more recent.
He said: "So far we are not talking about a theft, but about a loss.
"There is no doubt that this could not have happened without the participation of museum staff ... it is a stab in the back of the Hermitage, a stab in the back of all museums."
Police launched an inquiry but said there was a possibility that the pieces had simply been moved within the collection and their new location had not been catalogued.
Piotrovsky said the 221 missing pieces - worth some 130million roubles ($4.84 million) - had disappeared from a storeroom with very limited access.
Piotrovsky said: "Only three people could get in there. And many things were looked after by a guard who is no longer among the living."
Police told local news agencies it was too early to say what had happened to the exhibits, but prosecutors had opened an investigation under a law linked to "mass theft".
Residents of St Petersburg boast it would take a visitor 10 years to see all three million items in the museum's collection, which ranges from prehistoric art to one of the world's finest selections of impressionist and early 20th century paintings.
The theft of art treasures in Russia soared after the fall of the Soviet Union, with criminal gangs raiding some of the world's top museums for lucrative markets abroad.