"Today more and more often, under the guise of development of democracy and freedom, various ethnic nationalist groups are raising their heads. They take part in rallies, work on the Internet and among teenagers and students," Putin said.
He said ethnic aggression must be confronted and he rebuked local officials for failing to stop violence.
"We do not have the right to ignore any negative tendencies which arise in this sphere. We should understand that conflicts may not only weaken the state and society but destroy its
foundations," Putin said.
Putin was speaking at the first meeting of his Council on Inter-Ethnic Relations held August 24 in Saransk, capital of central Russia's Mordovia region.
Putin's comments come a day after nationalist football fans attacked supporters of a team from the Muslim North Caucasus province of Daghestan in Moscow and St. Petersburg.
Russia has seen several outbreaks of ethnic violence in recent years.
In December 2010, nationalist football fans rioted near the Kremlin, attacking non-Slavic passersby and clashing with police.
Russia is home to over 200 ethnic groups.