Police officers seized documents, electronic data storage devices and "some literature" from the library on Moscow`s Trifonovskaya Ulitsa, an unidentified law-enforcement official was quoted as saying by the capital`s Moskva news portal.
The search was prompted by claims the library stored newspapers that "distort historic facts" and exhibit a "Russophobic nature," the official said, Moskva reported.
Russia`s masked riot police officers blocked the entrance to the library on Thursday, Ukraine`s UNIAN news agency reported.
Russian police also searched the home of library director Natalya Sharina, seizing several books, she was quoted by UNIAN as saying.
The books confiscated from Sharina`s home included a volume on "Holodomor" — or "extermination by hunger," an artificially induced famine that killed millions of Ukrainians in the early 1930s during Soviet rule — according to the report.
Police also seized commendation notices issued by Ukraine`s former presidents Viktor Yushchenko, a Western-leaning leader, and Viktor Yanukovych, who was backed by Moscow, from the home of the library director, UNIAN reported.
The Ukrainian Foreign Ministry said the library search was a "crude and unmotivated" action by Russia`s authorities, which "once again confirm the aggressive policy by the Russian Federation against Ukraine."
Moscow annexed Crimea from Ukraine last year and supports the drive of pro-Russian separatists in the east of the country.