"Maus," by American artist and author Art Spiegelman, won a Pulitzer Prize in 1992 and was published in Russian in 2013.
But Varvara Gornostayeva, the chief editor at the book's publisher Corpus, said major bookstore chains were taking it off their shelves and Internet sites.
"They have removed the book," Gornostayeva told AFP. "It was selling very well and nobody had ever sent us any official complaints."
A reporter for Echo of Moscow radio, Darya Peshchikova, toured bookstores and said staff were expecting raids by the authorities ahead of May 9, when Russia marks 70 years since Soviet victory over Nazi forces in World War II.
"They are waiting for checks and decided to clean up their shelves," Peshchikova wrote on Twitter. "The reason is the swastika, employees say."
Russian authorities have moved to censor Nazi insignia, even raiding toy stores and antique shops which carry period paraphernalia, citing a law which forbids "Nazi propaganda" passed last December.
"There is no Nazi propaganda in it, this is a book that should be on the shelves on Victory Day," Gornostayeva argued.
"It's one of greatest anti-fascist books, with a deep and piercing message."
Maus tells the author's personal story of the Holocaust through the memories of his father, a Polish Jew who moved to the United States. It uses animal metaphors and minimalist graphic style, portraying Jews as mice and Germans as cats.
The Russian book's cover features two mice – a father and a son – and a stylized swastika image in the background, with the face of Hitler as a cat in the center. About 10,000 copies of the book have been sold in Russia, according to the publisher.
By Monday afternoon, three of Moscow's largest bookstores – Biblio Globus, Moskva, and Moskovsky Dom Knigi – had removed the book from their Internet stores.
Cached versions of store catalogues showed that all three carried it just a few days ago, but all denied this when contacted by AFP.
"It must be a mistake," said a woman in the PR department of Biblio Globus when asked why a days-old version of the store's webpage show the book as in stock.