Putin addressed ministers at a cabinet meeting to battle against "negative, racially motivated acts", which he said were becoming more frequent, Itar-Tass news agency reported.
"For Russia, a multi-ethnic country, this is absolutely unacceptable," he said.
Russian skinheads ransacked a Moscow market on Friday, trashing market stalls operated by people from the Caucasus region to Russia's south. Moscow police said they would press hooliganism charges against five of those detained.
Russian media also reported that a Chechen man was stabbed to death by a group of Russians shouting racial slurs in the center of the capital.
A front-page headline in the respected Kommersant business newspaper on Monday called the attacks "pogroms", a Russian word that has also entered the lexicon in other languages, referring to bloody Tsarist-era attacks on Jews.
Putin has often spoken out against racism and anti-Semitism, which have been on the rise in the decade since the fall of the Soviet Union. The president has appeared in public with ethnic minority and Jewish leaders to show his support.
But liberal critics say his hard-line stance towards separatism in Chechnya has helped fuel an atmosphere of hatred toward people from the Caucasus, which includes Georgia, Armenia and Azerbaijan as well as Russia's southern frontier.
Moscow city police had been on special alert for Hitler's birthday, which has been marked by racially motivated attacks in the past.
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