Officers were inspecting a property owned by a man suspected in a case of illegal arms possession and trafficking in Petergof, a suburb of Saint Petersburg famous for its tsarist palace.
"In the basement of the house, the officers uncovered a crocodile," the police statement said.
"No incidents involving the reptile occurred during the search" police said, adding that a veterinary service is now looking for a new home for the animal.
Pictures released by police showed the animal sitting in the dark, in a shallow muddy pool. Daytime temperatures in Saint Petersburg hovered around minus seven degrees Celsius (19 Fahrenheit), far below the preferred climate for the species.
The crocodile "has lived here since 2005," a neighbour told local television. "He was little at the time."
Police said they found items resembling ammunition that have been sent for analysis while the suspect is in custody.
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