Vladimir Filippov, the Russian education minister, said that the latest edition of Otechestvennaya Istoria XX Vek (20th Century National History), a ministry-approved text, was one-sided, negative and prejudicial to a "patriotic upbringing for pupils".
More than 500,000 copies of the book, by secondary school historian Igor Dolutsky, have been distributed since 1993, but it is the latest updated print run of 20,000, issued under ministry approval to 16 and 17-year-olds two years ago, that has attracted Mr Filippov's ire. The new edition includes Russian history up to early 2001, including Mr Putin's rise to power and election as president in 2000.
Quoting from comments by journalists and historians that Russia under Mr Putin has become more authoritarian and power more centralised, the book asks readers to discuss whether, in the words of left-of-centre Yabloko party leader Grigory Yavlinksy, "a police state was formed in Russia" in 2001.
Yavlinsky was referring to the strengthening of powers of the Federal Security Service, one of the successors to the KGB.
In the same year, independent TV station NTV was taken over by a Kremlin-connected gas monopoly, Gazprom, and its founder Vladimir Gusinsky was forced into self-imposed exile after a brief period of imprisonment.
Mr Filippov ordered a review of the book's accreditation after ministry officials, fearing that the section may influence young voters in next March's presidential poll, drew it to his attention.
Mr Filippov signed an order banning the book from Russian schools following a meeting of an official expert panel of historians last week. The panel lambasted the latest edition for its "subjectivity, one-sidedness and negativity".
The book was likely to increase the "psychological tension" of students and influence their opinion, rather than promote enquiry, the panel said in a statement released by the ministry of education.
Yelena Zinina, head of the education ministry's department for publishing, said that secondary schools would be banned from using it once an officially approved replacement was published.
The controversy has sparked a nationwide debate about the limits of legitimate enquiry in Russian schools.
Mr Putin told a meeting of historians that textbooks "should provide historical facts" and not become the battleground for competing political camps.
The newspaper Pravda suggested the ministry approve one official history text and that schools recommend others to achieve a balanced curriculum.