Investigators also raided the homes of library chief Natalya Sharina and a 75-year-old Ukrainian activist whose organisation has worked with the library, the activist told AFP.
The Investigative Committee said Sharina was charged with inciting ethnic hatred and violating human dignity by distributing books by radical nationalist Ukrainian author Dmytro Korchynsky, whose works are banned in Russia.
She faces up to five years in prison.
Officials searched the library and seized books that contained "anti-Russian propaganda," said the committee, which reports directly to President Vladimir Putin.
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"Our library does not offer publications which could incite ethnic strife," Vitaly Krikunenko said on radio.
The library provides access to "controversial" literature for historians, journalists and political scholars, he added.
On Wednesday, a dozen people including masked gunmen searched the apartment of Valery Semenenko, deputy chair of the Ukrainians of Moscow organisation, and seized books, discs and computers.
"They were looking for extremist materials," Semenenko told.
He added that he did not store Korchynsky's books, calling the raids an "excuse" for Russian authorities to pile pressure on Ukrainian activists.