The move was a response to a new law banning Nazi propaganda.
Russian bookstores began removing the Pulitzer Prize-winning Maus from their shelves due to the large swastika on its cover.
Concerns about raids by the authorities to remove the symbol ahead of May 9, when Russia will observe 70 years since the victory over the Nazis, reportedly led to the move on the graphic novel by Art Spiegelman.
Russia enacted a law banning Nazi propaganda in December. Toy stores and antique shops have been raided for Nazi symbols.
The Respublika bookstore chain confirmed to The New York Times on Monday that it had removed the book because it was concerned about the raids.
Inspectors seeking “book covers with Nazi symbols, in particular drawings of the swastika, led the company to consult with lawyers about the legitimacy of selling this book in our chain,” Anastasia Maksimenko, a representative for Respublika, told the Times in an email.
A spokesman for Russian President Vladimir Putin, while confirming that Nazi and fascist symbols were unacceptable, said that “everything needs to be in moderation.”
Maus, which won the Pulitzer in 1992, was first published in Russia in 2013, according to the French news agency AFP. About 10,000 copies have been sold in Russia, the publisher told AFP.